The restrictions, which also apply to Muslim-majority Kashmir, reflect a shift in India's foreign policy away from its long-held support for Palestinian liberation.
Canadian Prime Minister Justin Trudeau has accused the Indian government of being involved in the assassination of a Sikh leader on Canada's soil.
Taking questions at a news conference for the first time since he became India's leader in 2014, Modi did not outline specific steps to address rights violations.
American critics of India's leader say his movement's authoritarian bent is chilling dissent over his alarming approach to minorities and democratic principles.
“The fact that they continue to whitewash him by giving them a platform is very worrying,” said one human rights activist.
Tax department officials have searched the news organization's offices in New Delhi and Mumbai, weeks after the release of the controversial documentary.
The Indian government has dismissed the series, which is critical of Prime Minister Narendra Modi's role in the 2002 Gujarat riots, as "propaganda."
Clashes in India between Hindu nationalists and minority religious groups, particularly Muslims, have sparked tensions online and in person in the diaspora.
President Donald Trump received a warm welcome when he landed in India, but just miles away, protests rang out against the Indian Prime Minister Narendra Modi.
The ruling in the southern state of Karnataka comes after Muslims protested the ban, saying they were being deprived of their rights to education and religion.