Ottawa has expelled a top Indian diplomat as a result. Delhi has previously denied any involvement with Mr Nijjar’s murder.
Speaking in the House of Commons on Monday, Mr Trudeau said Canadian security agencies have been “pursuing credible allegations” linking “agents of the government of India” to Mr Nijjar’s murder.
“Any involvement of a foreign government in the killing of a Canadian citizen on Canadian soil is an unacceptable violation of our sovereignty,” he said.
He added: “Canada has declared its deep concerns to the top intelligence and security officials of the Indian government”.
Mr Nijjar, a prominent activist and vocal backer of an independent Sikh homeland, was gunned down outside a temple in Surrey, BC.
The killing set off protests against the Indian government in Canada and further afield, in London, Melbourne and San Francisco.
The incident has brought to light the demands of groups, including the separatist Khalistan movement.
Canada has the highest population of Sikhs outside their home state of Punjab in India. Sikhs make up about 2 per cent of India’s population.
Nijjar is third prominent Sikh to die in recent months
India has strongly opposed the Khalistan movement and claimed Mr Nijjar, 45, was a “terrorist” and led a militant separatist group, claims his supporters said were “unfounded”.
Mr Nijjar is the third prominent Sikh figure to have died suddenly in recent months – including the UK.
Avtar Singh Khanda, reportedly the head of the Khalistan Liberation Force, died in Birmingham in June.
According to the BBC, Mr Khanda’s death occurred in what has been described as “mysterious circumstances” that some believe could be related to poisoning.
A third man, Paramjit Singh Panjwar, was shot dead in May in Lahore, the capital of Pakistan’s Punjab province.
Mr Trudeau said his government has been working closely with Canada’s allies on the case.
He raised it with US President Joe Biden and Prime Minister Rishi Sunak.