Justin Trudeau has spoken a day after Canada withdrew 41 diplomats.
Trudeau however, did not confirm the FT report that India has asked Canada to withdraw 41 of 62 diplomats from the country.
Trudeau said the speaker of the House of Commons, who resigned Tuesday, was solely responsible for the invitation and recognition of the man but said it was a mistake that has deeply embarrassed Canada.
One can only hope that political and geopolitical games become outdated and the world works as one to solve the most pressing needs of humanity. Until then, a naturalised citizen will always have to prove something to the new country.
India had designated Nijjar as a terrorist in 2020.
Canadian Prime Minister Trudeau on Monday alleged the involvement of "agents of the Indian government" in the killing.
The Canadian Broadcasting Corporation first reported details of the intelligence.
Trudeau said that his government was not looking to provoke or cause problems.
The Canadian High Commissioner to India was summoned to the Ministry of External Affairs (MEA) and informed about the decision.
Trudeau said in Parliament that Canadian intelligence agencies have been looking into the allegations after Sikh leader Hardeep Singh Nijjar.