The development comes after the government abrogated provisions of Article 370 that gave special status to Jammu and Kashmir and Pakistan's subsequent attempts to internationalise the issue.
Besides bilateral issues, the two leaders discussed the regional situation.
An official release said that during the conversation, Modi highlighted the importance of creating an environment free from terror and violence in the region.
The conversation covered bilateral and regional matters and was marked by "warmth and cordiality which characterises the relations between the two leaders", the release said.
Modi recalled their meeting in Osaka on the margins of G-20 summit in June earlier this year and expressed the hope that the Commerce Minister of India and the US Trade Representative would meet at an early date to discuss bilateral trade prospects for mutual benefit.
"In the context of the regional situation, the Prime Minister stated that extreme rhetoric and incitement to anti-India violence by certain leaders in the region was not conducive to peace. He highlighted the importance of creating an environment free from terror and violence and eschewing cross-border terrorism without exception," the release said.
Modi reiterated India's commitment to cooperate with anyone who followed this path, in fighting poverty, illiteracy and disease.
Recalling that August 19 marks 100 years of Independence of Afghstan, the Prime Minister reiterated India's longstanding and unwavering commitment to "work for united, secure, democratic and truly independent Afghstan".
The Prime Minister stated that he appreciated remaining in regular touch with the US President.
Trump and Pakistan Prime Minister Imran Khan had a phone conversation last week in which the US President told him to resolve the Kashmir issue with India bilaterally.
( With inputs from ANI )