Addressing a media briefing, External Affairs Ministry spokesperson Arindam Bagchi said India also hoped that Canada will take action against separatists and anti-India elements.
Trudeau claimed that his public statement came after weeks of "quiet diplomacy" that included raising the allegations with India at the highest levels.
In an interview with The Canadian Press news agency, Canadian Prime Minister Justin Trudeau said he decided to make the allegations in public against India over the killing of Khalistani terrorist Hardeep Singh Nijjar to ensure a "further level of deterrence".
The government has rejected the allegations of its involvement in "any act of violence" in Canada, Minister of State for External Affairs V Muraleedharan said replying to a question.