India had accused Sandeep Sidhu of promoting Khalistani activities and playing a key role in the murder of Shaurya Chakra awardee Balwinder Singh Sandhu in Punjab in 2020.
Following the discontinuation of the SDS visa programme, students from all 14 countries, including India, will have to undergo more lengthy visa processes.
“The acts of violence at the Hindu Sabha Mandir in Brampton today are unacceptable; every Canadian has the right to practice their faith freely and safely," Mr Trudeau said in his X post.
The allegations were first reported by The Washington Post after Canada's Deputy Foreign Minister, David Morrison, confirmed Mr Shah's alleged role in a media leak to the Post.
India’s top exports to Canada include pharmaceuticals, gems and jewellery, textiles, and machinery, while Canada’s top exports to India include pulses, timber, pulp and paper, and mining products.