Prime Minister Justin Trudeau told Parliament on Monday that there were "credible allegations" of Indian involvement in the assassination of Sikh independence activist Hardeep Singh Nijjar, who had been wanted by India for years and was gunned down in June outside the temple he led.
Canada also expelled an Indian diplomat, and India followed by expelling a Canadian diplomat on Tuesday.
It called the allegations being investigated in Canada absurd and an attempt to shift attention from the presence of Nijjar and other wanted suspects in Canada.
"Important notice from Indian Mission: Due to operational reasons, with effect from 21 Sept. Indian visa services have been suspended till further notice," the BLS Indian Visa Application Centre in Canada said.
It gave no further details.
BLS is the agency that processes visa requests for India.
India's External Affairs Ministry did not immediately comment.
On Wednesday, the ministry issued an updated travel advisory urging its citizens travelling in Canada and especially those studying in the North American country to be cautious because of "growing anti-India activities and politically condoned hate-crimes".
Indians should also avoid going to venues in Canada where "threats have particularly targeted Indian diplomats and sections of the Indian community who oppose anti-India agenda", the ministry said.
Nijjar was working to organise an unofficial referendum among the Sikh diaspora on independence from India at the time of his killing.
He had denied India's accusation that he was a terrorist.
Demands for an independent Sikh homeland, known as Khalistan, started as an insurgency in India's Punjab state in the 1970s that was crushed in an Indian government crackdown that killed thousands.
The movement has since lost much of its political power but still has supporters in Punjab, where Sikhs form a majority, as well as among the sizeable overseas Sikh diaspora.
