In a subtle message to the Trudeau government over its perceived soft-stand on the Khalistan issue, Prime Minister Narendra Modi said today that those challenging India's sovereignty cannot be tolerated, even as India and Canada vowed to jointly combat terror threats, including from Sikh groups such as Babbar Khalsa.

After holding extensive talks with his Canadian counterpart Justin Trudeau, Modi, at a joint press event, also asserted that there cannot be any space for those who misuse religion for political motives and promote separatism.

A document on 'framework for cooperation on countering terrorism and violent extremism', finalised by India's National Security Advisor and the National Security and Intelligence Advisor of Canada, was also released after the Modi-Trudeau meet.

"They committed to work together to neutralise the threats emanating from terrorist groups such as al-Qaeda, ISIS, the Haqqani Network, LeT, JeM, Babbar Khalsa International, and the International Sikh Youth Federation," the document said.

While Babbar Khalsa International is a Sikh militant group based in Pakistan and which reportedly operates in Canada, Germany, the UK and some parts of India, the International Sikh Youth Federation is a proscribed outfit that aims to establish an independent homeland for the Sikhs of India.

Mincing no words, Modi also said, "There should be no space for those misusing faith for political goals and sowing seeds of division. Those who challenge sovereignty, unity and integrity of our countries cannot be tolerated."

Later, a joint statement said the two leaders reaffirmed the "breadth and scope" of Canada-India relations, based on the fundamental principle of respect for sovereignty, unity and territorial integrity of the two countries.

The statement as well as Modi's remarks come in the backdrop of Canada's  perceived pro-Khalistan approach, criticised by many including Punjab Chief Minister Amarinder Singh.

Trudeau's maiden India visit has been shrouded by controversies, including an invitation to convicted Khalistani terrorist Jaspal Atwal for yesterday's dinner by the Canadian High Commissioner to India. The invitation was later withdrawn.

After the talks, the two sides inked six pacts to boost cooperation in key areas including energy, information technology, trade, science and technology.

"Recognising that terrorism, violent extremism and radicalisation present acute challenges to global peace, stability and prosperity, the leaders resolved to combat terrorism and violent extremism in all their forms and manifestations," the joint statement said.

Welcoming the bilateral framework on anti-terror cooperation, the leaders also called for bringing terrorists to justice and holding accountable states sponsoring terrorism, including cross-border terror, in an apparent reference to Pakistan.

"They further emphasised that no country should allow its territory to be used for terrorist and violent extremist activities," the statement said. The leaders agreed to expand security cooperation through the NSA-level dialogue.

Modi said they reviewed the entire gamut of ties and identified ways to further strengthen them.

"We have decided to strengthen our defence cooperation. Terrorism and extremism are threats to democratic and pluralistic countries like India and Canada. It is important to come together to deal with these forces," he said at the joint press event.

Trudeau said as part of expanding the bilateral relationship with India, Canada will focus on security, including increased cooperation in the areas of counter-terrorism and peacekeeping among others.

Referring to Trudeau's visits to various parts of India in last six days, Modi said, "I am confident, Prime Minister Trudeau must have realised enthusiasm  and friendship towards Canada in India. He must have realised India's diversity and liveliness of our democracy."

The joint statement said Modi and Trudeau welcomed the continuation of uranium exports from Canada for peaceful use of civil nuclear power and agreed to expand the ongoing mutually-beneficial civil nuclear cooperation.

Trudeau also said, "Canada and India share a special friendship, and the agreements that we reached today will grow our middle class, create new opportunities for Canadians and Indians alike, and deepen the bonds."

The two leaders supported bolstering regional connectivity through transparent development of infrastructure and use of responsible debt financing while ensuring respect for sovereignty and territorial integrity, remarks seen as a message to China over its one-belt-one-road project.

Modi and Trudeau also reaffirmed the importance of the freedom of navigation and over-flight throughout the Indo-Pacific region, in accordance with international law, including the rights and jurisdiction of states under UNCLOS (United Nations Convention on the Law of the Sea), a clear reference to China's increasing military assertiveness in the Indo-Pacific region.

On trade and investment ties, Modi said instructions have been issued to negotiators from both the sides to redouble their efforts to finalise the proposed Bilateral Investment and Promotion Agreement and the Comprehensive Economic Partnership Agreement.