This was the second meeting between the two leaders after Modi was sworn-in on May 26 this year.
"The meeting was cordial and good. We talked about various issues," Rajapaksa told PTI after emerging from the over 30 minute-long meeting.
Asked about India pushing for expeditious implementation of the 13th Amendment, the President said, "The issue was not discussed in the meeting".
The 13th Amendment introduced provincial councils with specified powers based on the provisions of the Indo-Sri Lanka Accord of 1987.
Rajapaksa had earlier met with Modi in New Delhi after he travelled to India to attend Modi's swearing-in ceremony.
Modi had then noted that India valued its relations with Sri Lanka as the two leaders reiterated their desire to further strengthen bilateral relations.
The prime minister had also expressed interest in early launch of the 500 MW Sampur Coal Power project and greater connectivity between the two countries.
Photograph: Paresh Gandhi/Rediff.com