Krishna said earlier that he came bearing a message of "peace and friendship" but also called on Islamabad to act decisively against terrorism.
"We hope to discuss issues of mutual interest and concern that contribute to restoring trust and building confidence in our bilateral relationship," he said.
"I also look forward to receiving feedback on ... our core concern of terrorism, particularly in the light of the discussions our home minister had in Pakistan in the context of the interrogation of [David] Headley."
Headley, a US citizen, has pleaded guilty to working with Pakistan-based group, Lashkar-e-Taiba, to plan the attacks.
Accusations by GK Pillai, India's home minister, that Pakistani intelligence was behind the Mumbai attacksovershadowed the talks.
Pillai was quoted by the Indian Express newspaper on Wednesday as saying that evidence against Pakistan's Inter-Services Intelligence (ISI) emerged from the interrogation by Indian officials of Headley.
India has repeatedly demanded that Pakistan bring the perpetrators to justice and crack down on armed groups.
A Pakistani anti-terrorism court has charged seven suspects in connection with the violence, including alleged mastermind Zakiur Rehman Lakhvi and Zarar Shah, an alleged Lashkar operative, but Pakistan says it needs more evidence in order to prosecute others.
Pakistan is also likely to raise the issues of India's control of regional water resources and the divided Kashmir territory, where the Indian army is currently trying to quell protests after being accused of killing civilians.
India and Pakistan have fought two of their wars over the region and Kashmiri fighters have been battling New Delhi's rule for two decades in a conflict that has claimed tens of thousands of lives.
Raja Farooq Haider, the prime minister of Pakistan-controlled Kashmir, told Al Jazeera that Kashmiri fighters have not undertaken any attacks within India.
"The issue of Kashmir is a dispute between India and Pakistan. It is up to the people of Kashmir to decide their destiny," he said.
"If East Timor can get this right [to independence], why can't Kashmir get the right to self-determination?"
Analysts say Thursday's talks are unlikely to yield any concrete agreement beyond possible trust-building measures that could ease deep distrust.
India and Pakistan's prime ministers met in April on the sidelines of a regional summit in Bhutan, which set in motion the process of reviving suspended contacts at different levels of government.
The recent thaw has been encouraged by Western allies, in particular the US, which sees regional stability as key to winning the war in Afghanistan and has pushed Pakistan to fight Taliban fighters.