It was a rare, explosive allegation by the Canadian leader: That the Indian government killed a Canadian citizen who has advocated turning a part of India into an independent Sikh nation.

Prime Minister Justin Trudeau said on Monday that “agents of the Indian government” carried out the killing of a Sikh community leader in British Columbia last June.

Speaking in the House of Commons, Mr. Trudeau said that he raised India’s involvement in the shooting of Hardeep Singh Nijjar directly with Prime Minister Narendra Modi at the Group of 20 summit meeting earlier this month “in no uncertain terms.” He said the allegation was based on intelligence gathered by the Canadian government.

“Any involvement of a foreign government in the killing of a Canadian citizen on Canadian soil is an unacceptable violation of our sovereignty,” Mr. Trudeau told lawmakers. He said Canada would pressure India to cooperate with the investigation into the killing.

Mélanie Joly, the foreign minister, later announced that Canada had expelled an Indian diplomat whom she described as “the head” of Indian intelligence in Canada.

Mr. Trudeau said that the large community of Canadians of Indian origin had been angered by the killing and in some cases feared for their personal safety. There are an estimated 1.4 to 1.8 million Canadians of Indian heritage, many of whom are Sikhs. Their numbers include Jagmeet Singh, the leader of the opposition New Democratic Party, which is keeping Mr. Trudeau’s minority government in power.

The allegation that India’s government was involved in a calculated killing in Canada is likely to further corrode the already strained relations between the two countries. Earlier this month, Canada suspended negotiations on a trade deal with India that were scheduled to have been concluded this year. and during the G20, Mr. Modi excluded Mr. Trudeau from the list of leaders with whom he held formal bilateral meetings.

Mr. Nijjar, 45, was shot near a Sikh temple in Surrey, British Columbia. Investigators from the Royal Canadian Mounted Police said he was ambushed by masked men, but would not reveal whether the attack appeared politically motivated.

But Mr. Nijjar was known for his advocacy of the creation of an independent Sikh nation, Khalistan, that would include parts of India’s Punjab state, and India had declared him a wanted terrorist.

“If these allegations are true, they represent an outrageous affront to Canada’s sovereignty,” said Pierre Poilievre, leader of the Conservative Party. “Our citizens must be safe from extrajudicial killings of all kinds, most of all from foreign governments.”