New Delhi's move came after hundreds of protesters gathered in front of the Indian consulate in Vancouver, demanding an independent Sikh homeland.
India has summoned Canada's High Commissioner to "convey strong concern" over Sikh protesters in Canada and how they were allowed to breach the security of India's diplomatic mission and consulates.
According to Canadian media reports, hundreds of protesters gathered in front of the Indian consulate in Vancouver on Saturday over demands for an independent Sikh state, a simmering issue for decades recently triggered again.
"It is expected that the Canadian government will take all steps which are required to ensure the safety of our diplomats and security of our diplomatic premises so that they are able to fulfil their normal diplomatic functions," India's Ministry of External Affairs said in a statement on Sunday.
Canada has the highest population of Sikhs outside their home state of Punjab in India.
The statement follows Indian police on March 21 launching a hunt for Sikh preacher Amritpal Singh, who has revived talk of an independent Sikh homeland and stoked fears of a return to violence that killed tens of thousands of people in the 1980s and early 1990s.
READ MORE: India hunts preacher who revived calls for independent Sikh homeland
Police have accused Singh and his supporters of attempted murder, obstruction of law enforcement and creating disharmony and said he had been on the run since last week when officers tried to block his motorcade and arrest him.
Indian police also opened an investigation last week into a protest at its High Commission in London, where protesters with "Khalistan" banners took an Indian flag down from a first-floor balcony of the High Commission to denounce recent police action in India's Punjab state.
India summoned the top British diplomat in New Delhi last Sunday seeking an explanation.
Khalistan is the name of an independent Sikh homeland that some members of that community aspire to, both at home in India and in countries where Sikhs have settled.
READ MORE: Dozens arrested as Indian police hunt for Sikh separatist leader