Mr Modi said after the 90-minute bilateral talks that they discussed the challenges posed by terrorism. "There was great convergence in international matters. We discussed existing terrorism challenges including in south Asia and new threats in west Asia," he said.
The two countries have agreed to share intelligence and cooperate on counter-terrorism measures. They also discussed the need to dismantle "safe havens" for terrorists.
"India-US agree on joint & concerted efforts, including dismantling of safe havens for terrorist & criminal networks," MEA spokesperson Syed Akbaruddin tweeted after the meeting.
India-US agree on joint & concerted efforts, including dismantling of safe havens for terrorist & criminal networks- Syed Akbaruddin (@MEAIndia) September 30, 2014
But asked if India would join the US-led efforts to control the terror group Islamic State or IS in Iraq, senior MEA official Vikram Doraiswami said, "India is not joining the coalition".
The question had followed BJP leader Subramanian Swamy's tweet earlier in the day that Mr Modi had "committed to Obama that India would join the anti-ISIS war".
Happy that Modi committed to Obama that India would join the anti-ISIS war. Now Indo-US good relations will reach new unprecedented heights.- Subramanian Swamy (@Swamy39) September 30, 2014
Forty Indians are in IS captivity in Iraq and 40 countries have joined the US-led coalition against the group. Today Britain carried out airstrikes in Iraq. Two American journalists and a British aid worker have been beheaded by the terror group.
Regarding the beheadings, Mr Modi had said terrorism was an "unimaginable perversion". "Can you imagine a journalist being beheaded and it is being shown on television? We live in 21st century, and it's a challenge for us. It's a big challenge for us, which can shake us to the core," he had said on Monday at the Council of Foreign Relations in New York.
In the backdrop of Al Qaeda's recent announcement regarding a module in the Indian subcontinent, the Prime Minister had added, "In a recent interview, I told the CNN, the Indian Muslim will defeat the Al Qaeda's designs."