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Canada's Prime Minister Justin Trudeau, U.S. President Joe Biden and India's Prime Minister Narendra Modi talk while standing for a group photo with other leaders during the G20 summit at the Museum of Modern Art in Rio de Janeiro, Brazil, on Nov. 19.Ricardo Moraes/Reuters

Canadian security agencies believe Prime Minister Narendra Modi of India knew about the killing of a Sikh separatist leader in British Columbia and other violent plots, according to a senior national-security official who worked on the intelligence assessment of New Delhi’s foreign-interference operations in Canada.

The official said Canadian and American intelligence tied the assassination operations to Home Affairs Minister Amit Shah. Also in the loop, the official said, was Mr. Modi’s trusted national-security adviser Ajit Doval and External Affairs Minister Subrahmanyam Jaishankar.

While Canada does not have direct evidence that Mr. Modi knew, the official said the assessment is that it would be unthinkable that three senior political figures in India would not have discussed the targeted killings with Mr. Modi before proceeding.

The Globe and Mail is not identifying the official who was not authorized to discuss national-security matters.

This is the first time that Mr. Jaishankar had been connected to India’s foreign-interference operations.

In Brazil, where he was attending the G20 summit, Prime Minister Justin Trudeau said he had spoken to Indian officials about their country’s foreign-interference activities in Canada, especially the targeting of members of the pro-Khalistan movement that promotes an independent Sikh state in Punjab.

“In terms of engaging with the Indians, my priority is always to be standing up for Canadians’ safety and that is certainly the tenor of the conversations that I had,” he told reporters.

U.S. President Joe Biden pulled Mr. Trudeau and Mr. Modi together Tuesday for a discussion during the summit. It is not known what the three leaders said to each other.

The Privy Council Office said in a statement Tuesday that while the RCMP has said agents of the government of India have been involved in serious criminal activity in Canada, there “have been no allegations made by the Government of Canada against Prime Minister Modi, External Affairs Minister Jaishankar, or National Security Advisor Doval.”

Mr. Trudeau’s national-security and intelligence adviser Nathalie Drouin and David Morrison, a deputy minister at Global Affairs, told The Washington Post last month that Mr. Shah was implicated in the gangland slaying of Sikh separatist leader Hardeep Singh Nijjar.

The information given to The Washington Post included linking India to the slaying of Sikh activist Sukhdool Singh Gill, who was shot in Winnipeg on Sept. 20, 2023. Mr. Gill was killed two days after Mr. Trudeau announced in the House of Commons that Canada had credible evidence that India was behind the June, 2023, slaying of Mr. Nijjar.

RCMP Commissioner Mike Duheme said on Oct. 14 that evidence shows India was involved in the killing of three people, but he identified only the slaying of Mr. Nijjar. Commissioner Duheme said eight people have been charged with murder and 22 with extortion. Four Indian nationals have been charged in the killing of Mr. Nijjar outside a Sikh temple.

That same day, Canada expelled six Indian diplomats, including High Commissioner Sanjay Kumar Verma, leading to an even deeper rupture in bilateral relations.

In testimony before the Commons committee on public safety and national security last month, Ms. Drouin said the leak to The Washington Post was part of a communications strategy that she and Mr. Morrison came up with to ensure a major U.S. publication got Canada’s side of its continuing foreign-interference dispute with India.

As The Globe reported, the RCMP went to the government in late August to ask for an all-out effort to convince India to end its hostile foreign-interference campaign. The Mounties were concerned that 13 Canadians were in imminent danger and the scale of India’s activities could not be stopped solely by law enforcement.

Ms. Drouin told the committee that the RCMP asked to travel to New Delhi on Oct. 8 to present evidence, but India “used an administrative technicality to block this meeting.” The RCMP then travelled to Washington on Oct. 10, but “while an India officer confirmed the meeting they never showed up.”

A meeting was eventually set up on Oct. 12 in Singapore at which Ms. Drouin, Mr. Morrison and deputy RCMP commissioner Mark Flynn presented evidence to Mr. Doval, the national-security adviser to Mr. Modi. Ms. Drouin testified that Mr. Doval rejected all of Canada’s requests to resolve the issue, leading the federal government to announce on Thanksgiving Day that it had expelled six Indian diplomats. New Delhi responded by ordering six Canadian diplomats to leave the country.

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