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David Vigneault, director of the Canadian Security Intelligence Service, appears on Parliament Hill, on June 13, 2023.Justin Tang/The Canadian Press

A federal watchdog agency says an active overseas clandestine spy service operation was abruptly halted by a top adviser to former prime minister Justin Trudeau, a decision it says needlessly put CSIS officers in danger.

In a report released Thursday, the National Security and Intelligence Review Agency, or NSIRA, said it had investigated a 2022 Canadian Security Intelligence Service operation that was suspended before later being authorized to proceed.

NSIRA said the national security and intelligence adviser to the prime minister at the time stopped the “active operation,” a measure that “created unnecessary danger for the CSIS team,” according to its heavily redacted report.

The 43-page report from NSIRA, an independent body that oversees federal intelligence agencies, provides a rare glimpse inside the political oversight of intelligence operations.

Jody Thomas, a former deputy minister of national defence, was national security adviser in 2022.

NSIRA said the decision to halt the operation was not made by then-CSIS director David Vigneault, and there was no written record that then-public safety minister Marco Mendicino had stopped it. Those two would have been the only ones with statutory authority to approve, reject or halt operations.

While the mission was ultimately allowed to proceed, NSIRA said the suspension of an active operation “caused harm to Canada’s international reputation” and “raises concerns regarding CSIS’s accountability mechanism.”

The report does not offer any details on the nature of the operation or its location, but CSIS is allowed to carry out disruption activities and confidential source handling in other countries as long as it relates to a threat to Canada’s security.

Ms. Thomas told The Globe and Mail on Thursday that NSIRA had not reached out to get her side of what had transpired. She said she was asking questions about the operation on behalf of many parts of government, including the departments of Global Affairs and Public Safety.

She said she didn’t personally halt the operation.

“This is a CSIS perspective on how things unfolded and I can’t talk any more about it than that because of the nature of the security of the operation,” she said of the NSIRA report findings. “The operation had some questions asked about it that were from other levels of government, more senior levels of government, and I was the conduit of that information as opposed to me personally stopping the operation.”

Ms. Thomas said the questions that were asked about the sensitive operation would not have been necessary had CSIS more thoroughly informed Mr. Mendicino. The former minister is now acting chief of staff to Prime Minister Mark Carney.

“I ensured the questions got answered and then the operation proceeded and concluded,” she said. “It should have happened before it started,” she said of the questions posed to CSIS.

“I think it is a lesson that when you are conducting complex information or complex operations, agencies and departments have to be forthcoming so that decision makers understand the risks of what’s being done.”

NSIRA’s review says that CSIS had difficulty grappling with the halt to the operation, “so much so, in fact, that management and control of the operation appeared to cease functioning properly.”

The report said it appeared that the CSIS director “no longer had decision-making control over the active operation.” NSIRA quoted an e-mail Mr. Vigneault sent to senior government officials: “time is running out and the situation is getting much more tense on the ground. We need a decision tomorrow.”

Dan Stanton, a former senior manager at CSIS who is now director of the national-security program at the University of Ottawa, said he has never seen an instance before of something akin to political intervention in a continuing operation.

“You can’t have the prime minister’s adviser just calling the whole thing off,” he said. “Once it’s a go, you can’t have someone else saying later, stop it.”

The way the operation was handled would cause reputational damage with CSIS among its allied spy partners, he said.

Mr. Stanton said it was “appalling” to see Mr. Vigneault having to beg for approval.

“I mean, he should be the one making that call. In a way it is undermining his authority.”

In the report, NSIRA faulted CSIS for failing to properly brief Mr. Mendicino and other senior government security officials on the nature of the operation.

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