Canadian Prime Minister Justin Trudeau has acknowledged the presence of Khalistan supporters in Canada but said they do not represent the Sikh community as a whole.

His comments came during Diwali celebrations at Ottawa's Parliament Hill recently amid an ongoing diplomatic row with India over the killing of Khalistan extremist Hardeep Singh Nijjar.

“There are many supporters of Khalistan in Canada, but they do not represent the Sikh Community as a whole. Similarly, there are supporters of Prime Minister (Narendra) Modi's government in Canada, but they do not represent all Hindu Canadians,” Trudeau said.

The relations between the two countries came under severe strain following Trudeau's allegations in September last year of a "potential" involvement of Indian agents in Nijjar's killing.

New Delhi rejected Trudeau's charges as "absurd".

India expelled six Canadian diplomats and withdrew its high commissioner Sanjay Verma and other "targeted" officials from Canada after strongly dismissing Ottawa's charges.

India has been maintaining that the main issue between the two countries is that of Canada giving space to pro-Khalistan elements operating from Canadian soil with impunity.

Last week, Khalistani supporters disrupted a consular event co-organised by the Hindu Sabha temple in Brampton and the Indian Consulate.

The incident was condemned by Trudeau who said every Canadian has the right to practise their faith freely and safely.

In a statement, the Ministry of External Affairs said that New Delhi remains "deeply concerned" about the safety and security of Indian nationals in Canada.

The Indian consulate in Toronto said it was scrapping some of the planned consular events this month because of Canadian “security agencies conveying their inability to provide minimum security protection” to organisers.