Canadian police have arrested three men on suspicion of killing a Sikh separatist leader last year, and say they are investigating the suspects' possible ties to the Indian government.

The religious leader was fatally shot in western Canada in June last year. He was a Canadian citizen and reportedly a supporter of the independence movement in northern India. The three suspects are Indian citizens.

Canadian Prime Minister Justin Trudeau has accused the Indian government of involvement in the fatal shooting.

Canada's federal police told reporters on Friday they had arrested three Indian nationals in their 20s for their alleged roles in the murder.

The police said the suspects stayed at a house in the city of Edmonton in Alberta, about 800 kilometers from where the Sikh leader was shot to death.

The police declined to provide details of evidence or possible motives, saying they suspect others may also be involved.

Canadian authorities have already expelled an Indian diplomat who allegedly played a part in the killing.

India denies the accusation and has moved to retaliate against Canadian diplomats in India. Amid worsening bilateral ties, Canada has withdrawn diplomats and their families from India, citing security concerns.