Three men were arrested Friday and charged in the killing of a Sikh leader in British Columbia, which Prime Minister Justin Trudeau accused India of orchestrating, fraying relations between the two countries.

Hardeep Singh Nijjar, a Sikh nationalist and Canadian citizen, was gunned down last June by two masked assailants in the parking lot of the temple in Surrey, British Columbia, where he was president, according to the police.

Three men, all Indian nationals in their 20s, were all arrested in Edmonton, Alberta and charged with first-degree murder and conspiracy to commit murder. Police identified the men as Karan Brar, Kamalpreet Singh and Karanpreeet Singh.

The police said the men had been living in Canada three to five years and were not permanent residents of Canada, but would not comment on their immigration status.

Several other investigations are ongoing and include exploring links to the Indian government’s involvement, said Assistant Commissioner David Teboul of the Royal Canadian Mounted Police, adding that the relationship with Indian investigative partners had been challenging.

Mr. Nijjar was a leader in the local Khalistan movement, which seeks to create a separate Sikh nation in India that includes the northern state of Punjab.

He was born in Punjab and moved to Canada in the heat of India’s crackdown on Sikh leaders in the 1990s, according to Indian media reports. He was the leader of the Guru Nanak Sikh Gurdwara temple in Surrey, a city outside Vancouver that is home to one of the largest Sikh populations in Canada.

The Indian government had labeled Mr. Nijjar a terrorist in 2020, and called for his arrest.

His killing set off diplomatic skirmishes between Canada and India, after Mr. Trudeau accused India of being involved in the killing on Canadian soil. The Indian government strongly denied the accusation, which led both countries to expel senior diplomats.

Mr. Nijjar had been one of several Sikh community members warned about threats on their life by the Royal Canadian Mounted Police.

Jagmeet Singh, leader of the federal New Democratic Party who represents a British Columbia district, testified last month at a foreign interference inquiry that he had also been warned by the police of potential threats against his life.

The public inquiry, which delivered its interim report on Friday, was established last September following increasing political pressure against Mr. Trudeau to investigate allegations that countries like China and India have interfered in Canadian elections.

The report found that Indian intelligence officials use proxies in Canada to influence communities and politicians, with a special interest in the Khalistan movement.

The arrest of the men accused of carrying out Mr. Nijjar’s killing will provide little comfort to the Sikh community if Indian officials implicated in the killing and other interference activities are also not held accountable, said Balpreet Singh Boparai, a Toronto-based lawyer at the World Sikh Organization of Canada.

“We just hope that Canada has the guts to be transparent and identify those individuals who are behind this plot,” he said.

Other than a map outlining the getaway vehicle’s route and some grainy images of the assailants, the police investigating Mr. Nijjar’s murder over the last year have released little information on their progress.

In December, sources who spoke to The Globe and Mail, a Canadian newspaper, said arrests were imminent, but the passing months had left some in the community concerned that Mr. Nijjar’s one-year death anniversary in June would pass with no resolution.

“We would not be at this point without the bravery and the courage of the Sikh community coming forward,” said Superintendent Mandeep Mooker, a homicide investigator for the Mounties.

Mihika Agarwal contributed reporting from Surrey, British Columbia.