Harper's annual Arctic tour in August 2011 was embarrassed when a First Nations group issued a news release saying the federal government had suspended water-quality sampling at 21 sites in the North.
Speaking in Haines Junction, Yukon, the prime minister quickly doused the controversy by saying the move was "not authorized" and that Environment Minister Peter Kent had ordered water sampling to resume once he found out about it.
There was no explanation at the time about why apparently rogue department officials made a policy change for which they had no authority, leaving Kent blindsided.
But a 600-page internal file on the controversy, obtained by The Canadian Press under the Access to Information Act, shows the officials had in fact received a green light from senior levels at Environment Canada.
They also indicate Kent was aware of the proposed cuts weeks before they were implemented.
The emails, memos and other materials provide a glimpse inside a public service that has often been on the losing end of high-profile clashes with the Harper government.
The file shows that the review of water-monitoring across Canada began in 2010, after the federal commissioner of the environment issued a report saying the department needed to re-assess the program to place it on a more scientific basis, taking into account risks. The review was publicly endorsed by then-environment minister John Baird.
The department was later hit with severe budget cuts in 2011, prompting officials to temporarily suspend water monitoring in the north while it reviewed potential risks, to ensure sampling was taking place at the most appropriate locales.
The proposed suspensions were outlined to senior Environment Canada officials months in advance, and warnings were given to the government of the Northwest Territories and even Kent himself, the file shows.
The post-mortem on the controversy also contains no reference to authorization issues, as raised by Harper, referring only to the need for improved communications.
"The mis-communication with partners and stakeholders was a lesson learned," says one document. "A communication strategy will be developed to ensure all are properly informed."
The Northwest Territories minister responsible for the environment, J. Michael Miltenberger, alerted Kent himself to the potential problems with water-quality monitoring early in the summer.
In a June 27, 2011, letter to Kent and Aboriginal Affairs Minister John Duncan, Miltenberger wrote: "Recently, operational GNWT (Government of the Northwest Territories) staff have been made aware of proposed federal government reductions to water quantity and quality monitoring programs in NWT."
Miltenberger pressed Kent and Duncan not to proceed.
"I had opportunity to talk to minister Kent when he was here a number of weeks ago," Miltenberger later told the N.W.T. legislature in Yellowknife, on Aug. 24.
"These cuts are going to be felt across the land. They're going to be felt in the Northwest Territories."
Spokespersons for Kent and Environment Canada did not respond to questions about the discrepancy between Harper's remarks and a paper trail indicating staff had full authority for their decisions, and that the minister was made aware of the cuts in advance.
"To respond, the minister of the environment took action to ensure that water-monitoring resumed at suspended sites," department spokesman Mark Johnson said in an email.
"Environment Canada is committed to delivering a scientifically-robust water quality monitoring service in the North."
In an interview last week, Miltenberger said that as far as he knows, the 21 monitoring sites remain up and running a year after the incident.
Water-monitoring in the North is more important than ever, he said, because airborne exotic chemicals — such as heavy metals — as well as oil and gas development threaten the environment more than ever as climate change melts more Arctic ice.
"We need to have that baseline information so that as development occurs, we can compare," he said.
Environment Canada withheld the 600-page file requested by The Canadian Press for more than six months beyond the legislated deadline, prompting a complaint to the information commissioner of Canada.
Harper's own department, the Privy Council Office, refused to release a one-page briefing note about the incident to the prime minister, citing exemptions in the Act referring to federal-provincial affairs and advice.