Prime Minister Stephen Harper’s government is offering no explanation for a mysterious memo sent from a senior bureaucrat to the environment minister that incorrectly summarized scientific evidence from a secret report.

The memo, released through a court challenge, contradicted the warnings from an Environment Canada scientist about “imminent” danger from a major residential real estate project near Montreal that is threatening the survival of a critical population of western chorus frogs, protected under federal endangered species legislation.

The $300 million real estate project in La Prairie, a suburb on the south shore of Montreal, could cause the extinction of regional populations of the species, according to a report that was marked “secret” and authored by Environment Canada scientist, Alain Branchaud. The report, dated December 13, 2013, identified the region as a “high-priority” conservation area for the tiny amphibian that is small enough to fit on a toonie.

His conclusions were highlighted in a draft memo that circulated within Environment Canada in February 2014.

“The Department’s assessment is that the development project constitutes an imminent threat to the recovery of the Western Chorus Frog, but not to its survival (in other regions such as Ontario),” said the memo, addressed to Environment Minister Leona Aglukkaq.

“You have the legal obligation to make the recommendation (to cabinet) for an emergency order if you are of the opinion that the species faces imminent threats to its survival or recovery.”

Aglukkaq didn’t respond to questions, sent to her directly on Twitter and through her office, asking what happened to the scientific advice and whether she read the internal memo with the correct information. Her office also declined to respond to a question asking whether anyone among her staff had viewed this memo.

A second memo, dated March 12, 2014, in the middle of a Quebec provincial election campaign, contradicted the scientific evidence from the previous memo. Instead it said that the $300 million project wasn’t a threat to the recovery of the western chorus frog.

The documents have surfaced through legal proceedings launched in Federal Court by Nature Québec, a conservation group based in Quebec City, and the Centre québécois du droit de l’environnement, a Montreal-based legal organization that promotes the enforcement of environmental laws.

They also show that department officials prepared a presentation for the staff of former environment minister Peter Kent on July 4, 2013, that included a public relations analysis of media coverage of the issue.

“It’s incredible,” said Christian Simard, president of Nature Québec and a former federal MP, in an interview. “The documents read like a novel and at the same time it shows us just how much something is rotten in the state of Denmark, as (Shakespeare’s play) Hamlet would say.”

Branchaud’s analysis noted that the species had declined about 40 per cent in both Ontario and Quebec since the mid-1990s.

The western chorus frog, which plays important economic and ecological roles in the food chain such as controlling insect populations, is disappearing because of threats such as urban sprawl, pesticides, intensive agricultural development and climate change, according to a federal recovery strategy posted online in July. The recovery strategy also included La Prairie in a list of municipalities with critical habitat for the threatened amphibian.

Environment Canada declined interview requests with the scientist, Branchaud. It also declined an interview request with assistant deputy minister Mike Beale, who, according to internal emails released by the government, was overseeing the drafting of the memos before leaving on a trip to Europe.

“Not sure I’m happy with everything I’ve done and am still thinking through the issues. Have a good weekend!” – Robert Mclean, executive director of the Canadian Wildlife Service.

A statement filed by the environmental law organization in court on Sept. 24 accused bureaucrats of “deleting and altering” scientific data collected by Branchaud after the scientist had produced a “complete, methodical, and objective scientific analysis” about the impact of the real estate development on the western chorus frogs.

A senior manager in the department, sent the department’s legal counsel, Natasha Gaydamack, a revised version of the memo in an email, also sent to other bureaucrats, on Feb. 28, 2014 after a phone conversation.

“Further to your call today, I’ve revised the MTM (memo to the minister) and drafted a couple of letters (all in the one Word doc),” wrote Robert Mclean, executive director of the Canadian Wildlife Service in the email. “Not sure I’m happy with everything I’ve done and am still thinking through the issues. Have a good weekend!”

The federal and provincial governments subsequently allowed work on the real estate project to begin, despite concerns raised by conservation groups that the municipality wasn’t respecting existing conditions of its permits. The government officials also stood by their approvals following complaints that triggered an investigation into whether there was logging on the site that allegedly violated federal legislation enforcing an international treaty that protects migratory birds.

The department said it couldn’t provide comments since the matter was in court.

Environment Canada previously confirmed to Montreal newspaper La Presse, in a report published on July 10, 2014, that its enforcement branch had opened the investigation into those alleged violations of the law protecting migratory birds, which could result in fines of up to $1 million or up to three years in prison if there is a conviction.

The department confirmed on Friday that it had received complaints about logging and sent two agents from its wildlife enforcement directorate to the site on July 8, 2014. Environment Canada also said that the file was still under investigation.

A manager from Environment Canada, Jonathan Campagna, who identified himself as being responsible for “intelligence” in the federal department’s wildlife enforcement division, told a local environmental project manager, Tommy Montpetit, in a mid-July email that the government was still allowing work to proceed on the site, despite the investigation, requiring only that the workers stop cutting trees until mid-August.

Montpetit, who also contributed to the federal recovery strategy for the western chorus frog, published in July, was stunned.

“It’s like telling someone they are driving under the influence but they can go home,” said Montpetit, who has worked on conservation issues for nearly 20 years. “It’s completely amazing. I’ve never seen anything like this.”

Timeline of events:

May 15, 2013

Nature Québec president Christian Simard and two other citizens wrote to former environment minister Peter Kent asking him to recommend that the federal government use its emergency powers to protect the habitat of the western chorus frogs from the real estate development project proposed in La Prairie, near Montreal. Simard based his request on information obtained from minutes of a federal and provincial meeting in which experts from both governments, including Environment Canada, raised concerns about the threat to the species from the residential project.

July 4, 2013

Environment Canada’s Canadian Wildlife Service prepared a presentation for former minister Kent’s staff about the western chorus frog as well as a public relations analysis of media coverage of the issue, related to the real estate development project in La Prairie, Quebec.

July 15, 2013

Prime Minister Stephen Harper shuffled his cabinet and demoted Kent, replacing him with Leona Aglukkaq as environment minister.

October 16, 2013

After receiving no response or acknowledgment of their request from either Kent or his successor, Aglukkaq, Nature Québec sent a lawyer’s letter to the new environment minister to reiterate their request for an emergency protection order.

Nov. 14, 2013

Sue Milburn-Hopwood, director general of the Canadian Wildlife Service at Environment Canada, responded to Simard and others, explaining that the government was reviewing the case.

December 11, 2013

Andrea Lyon, then the associate deputy minister at Environment Canada, signed a memo to Aglukkaq informing her about the case, indicating that the recovery strategy for the western chorus frog was scheduled to be released in March.

December 13, 2013

Environment Canada scientist Alain Branchaud authored an analysis that warned the real estate project would threaten the recovery of the western chorus frog.

February 7, 2014

Internal Environment Canada emails indicated that department officials provided an update to Bryan Macleod, a political staffer in Aglukkaq’s office, informing him that former premier Pauline Marois’s Parti Québécois government was going to authorize permits within days for the real estate development. A bureaucrat recommended putting other details about the case in the note to the minister but Mike Beale, an assistant deputy minister asked if the bureaucrat could “shorten” the message “a lot” and only provide more information if the minister’s office asked follow up questions.

Feb 9, 2014

Milburn-Hopwood sent a draft version of a memo to Beale that summarized scientific evidence in support of an emergency order to protect the habitat of the chorus frog. The memo, addressed to Aglukkaq, said she was obligated to recommend that cabinet issue an emergency order to protect the western chorus frog if she believed there was an imminent threat either to its recovery or survival.

Feb. 28, 2014

The executive director of the Canadian Wildlife Service, Robert Mclean, emailed the department’s legal counsel, Natasha Gaydamack, a revised version of the memo for the minister – contradicting the scientific assessment by Branchaud. In his email, also sent to other bureaucrats, Mclean wrote: “Further to your call today, I’ve revised the MTM (memo to the minister) and drafted a couple of letters (all in the one Word doc). Not sure I’m happy with everything I’ve done and am still thinking through the issues. Have a good weekend!”

March 1, 2014

Millburn-Hopwood sent an email to other bureaucrats writing:

“I talked with Mike (Beale) today and he wants a letter and note along the lines we discussed earlier in the week. I have drafted what I think we should send. Mike wants to see Monday morning before he leaves for Europe.”

Beale also sent Millburn-Hopwood an email saying he wanted to sign off on the memo on the Monday.

March 5, 2014

Former Parti Québécois premier Pauline Marois asked the lieutenant governor to dissolve the National Assembly and call a general election.

March 12, 2014

The final version of the memo – contradicting the scientific assessment done by Environment Canada’s Alain Branchaud – is stamped with this date. The memo was signed by then associate deputy minister Andrea Lyon. The name of then deputy minister Bob Hamilton also appeared on that memo.

April 7, 2014

Quebec Liberal Leader Philippe Couillard was elected with a majority of seats in the National Assembly and became the province’s new premier.

July 3, 2014

Environment Canada published its recovery strategy for the western chorus frog after Montreal newspaper La Presse reported on a draft version of the strategy. The recovery strategy listed La Prairie as one of more than a dozen municipalities with critical habitat for the species. The strategy was subject to a two month review for public comments of consultations that ended in September.

July 8, 2014

Two agents from Environment Canada’s Wildlife Enforcement Directorate inspected the La Prairie site following complaints about logging that may have allegedly violated a federal law enforcing an international treaty protecting migratory birds.

July 10, 2014

Environment Canada confirmed to La Presse reporter Éric-Pierre Champagne that it launched an investigation, under the federal legislation, over alleged harm to bird nests from cutting trees at the site of the project. The developer agrees to stop cutting trees until August 15.

Sept. 24, 2014

The Centre québécois du droit de l’environnement filed a report in Federal Court asking it to intervene in the case.

October 2-3, 2014

The office of Leona Aglukkaq and the minister herself fail to respond to questions from the media about the case. Environment Canada takes more than 31 hours to respond to a question about the investigation into alleged harm to migratory birds, but then confirmed that it was still investigating these allegations. Any violation of this federal law could be punishable by a fine of up to $1 million or up to three years in prison.