Kerry's meeting with Modi at the Prime Minister's House, 7, Race Course Road, comes a day after he met External Affairs Minister Sushma Swaraj for the 5th India-US Strategic Dialogue.
Kerry, who in his speech Thursday said the US was keen to partner the Modi government in its vision of "Sabka saath sabka vikas" or development for all, met Modi at 11 a.m.
Kerry arrived here Wednesday at the head of high-level delegation, in the first high-level contact of the US with the Modi government.
During the Kerry-Sushma meeting Thursday, India raised the issue of America's cyber snooping and termed it unacceptable between friends.
Addressing a joint press briefing after their over three-hour long talks, Sushma Swaraj said she had conveyed to Kerry that the people of India were very agitated over the US surveillance activities.
Kerry, in his reply, said that the US "fully respects and understands the feelings expressed" by the minister and that the US would continue to work with India wherever they saw a threat to their shared interests.