"There should be no place for people who use religion for political purposes and to divide people. Those challenging sovereignty, unity and integrity of our countries cannot be tolerated," Modi said as he issued press statement with Trudeau.
The visit of Canadian leader has marred by controversy with the presence of convicted Khalistani terrorist Jaspal Atwal at his Mumbai reception.
Trudeau, who is on a week-long visit to India, met Modi today to hold talks on energy, education, healthcare, IT, start up, science & technology, defence and security, tourism and people-to-people contacts.
"We have agreed to strengthen our security cooperation. Terrorism and extremism are threats to democratic, pluralistic societies like India and Canada. It is important for us to come together to combat these forces," Modi said after the talks.
After the talks, the two countries signed six agreements in the field of higher education, atomic energy, ICT, IPR, energy and sports.
The ties between India and Canada have been on an upswing. Approximately 1.4 million Canadians are of Indian heritage and India is Canada's second largest source of immigrants.
"We are committed to build friendly relations with Canada's Indian community and seeking their active participation in India's progress. India-Canada relationship is a natural partnership of shared values. I hope to have more robust partnership between the two countries and the bright future of our two countries," Modi said.
Canada is also a leading education destination for Indian students, and India is the second largest source of international students, an estimated 124,000 in 2017, as per official figures.
Trudeau said India is a natural partner of Canada as it looks for new opportunities to do business beyond its boundaries.
"As Canada looks to diversify its own economy and looks for new opportunities to do business beyond its boundaries, India is a natural partner and a trusted friend for commercial cooperation," he said.
"We share not only rich a history but a set of values that encourage a natural friendship between our two countries," he said.