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Freeland said she was quitting in the wake of a meeting last Friday with Trudeau, who asked her to take on a lesser post after the two had been arguing for weeks over spending.
India-Canada ties remain deeply troubled over Canada's allegation of India's involvement in the killing of Nijjar.
Dalla was designated as a terrorist by India in 2023.
The move comes amidst an ongoing diplomatic dispute between India and Canada.
The MEA said Canada's actions highlighted their hypocrisy when it comes to freedom of speech.
The Peel police have charged three people in association with the violence.
Despite the disruption, the High Commission highlighted that consular staff successfully issued over 1,000 life certificates to Indian and Canadian nationals.
A spokesman for the Peel Regional Police told AFP that no arrests had been made.
MEA also summoned a Canadian diplomat to express New Delhi's protest regarding the issue.
The Indian government did not immediately respond but has dismissed Canada's prior accusations as baseless, denying any involvement.
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