Prime Minister Justin Trudeau joined Conservative Leader Pierre Poilievre and NDP Leader Jagmeet Singh at the Khalsa Day rally in Toronto on Sunday.
The rally commemorates the Sikh faith, and some participants chanted and carried banners emblazoned with slogans calling for a state separate from India, known as Khalistan.
India formally summoned Canada's deputy high commissioner Monday, and the country's foreign ministry decried what it called "disturbing actions being allowed to continue unchecked at the event."
India's foreign ministry didn't specify what it took issue with, but noted there were displays of separatism and alleged this illustrates Canada tolerating "extremism and violence."
New Delhi and Ottawa have been at odds over the issue for decades, and the relationship has been significantly strained since Trudeau accused India of playing a role in the slaying of a Canadian Sikh leader last year.
Canada insists it will not infringe on free speech, including when Sikh people call for the existence of Khalistan.
But India says these comments violate its constitution.
India has pointed out instances of people in Canada openly glorifying those linked to the 1985 bombing of an Air India plane, whose passengers were largely Canadian citizens.
Human-rights groups says the country's Hindu nationalist government has increasingly persecuted minorities in recent years.
Foreign Affairs Minister Mélanie Joly's office did not immediately comment on India's rebuke Monday.
Joly has repeatedly said she wants to navigate the diplomatic rift with India in private.
