After the meeting between their leaders, the two sides signed four pacts, including one for air services and cooperation in merchant shipping.
At a joint media event with the Cypriot leader, Mr Modi said India has always stood with Cyprus on crucial issues and firmly supports its sovereignty, unity and territorial integrity.
Noting that they had "detailed discussion" on bilateral as well as regional and international issues of mutual interest, PM Modi said, "We agreed on the need for all countries to decisively act against states that generate, support, shelter and sustain violence factories in our regions."
The two sides also agreed on the need of early reforms of the UNSC, Mr Modi said and expressed India's appreciation for Cyprus' support to India's bid for inclusion in it as a permanent member.
Earlier, External Affairs Minister Sushma Swaraj called on the Cypriot president, and discussed areas of bilateral cooperation.
Earlier, Mr Anastasiades was accorded a ceremonial welcome at Rashtrapati Bhavan today.