Kerry said it was important that Islamabad moved to "deprive any group of sanctuary", highlighting the threat posed by Lashkar-e-Taiba, a Kashmiri separatist group which is allegedly behind a string of anti-Indian attacks.
"We will not and we cannot make distinctions between good and bad terrorists... Terrorism is terrorism," Kerry said at a press conference alongside India's External Affairs Minister Sushma Swaraj.
Kashmir unrest sparks Pak-India diplomatic spat
Kerry said the US government had "had conversations with all members of the region frankly about efforts they need to take against terrorism which comes out of their country", adding that he had personally raised the issue with Prime Minister Nawaz Sharif.
Around 70 civilians have been killed since the beginning of last month in the aftermath of the Indian army's killing of a charismatic young separatist leader and a curfew remains in place in many parts of held Kashmir.
Swaraj said there was "a meeting of minds" during her talks with Kerry on tackling the threats posed by extremists as she reiterated long-standing accusations that Pakistan was sponsoring "cross-border terrorism".
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"I briefed Secretary Kerry about the continuing problem of cross-border terrorism that India and the larger region faces from Pakistan," she said.
Both sides said that there had been an agreement to step up cooperation on intelligence.
"We agree on additional measures to strengthen our counterterrorism," said Swaraj. "We will intensify intelligence sharing."
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