India's SM Krishna agreed that the talks were just a beginning.
"We are starting on this journey cognoscente of the complexities in our relations, the challenges that lie ahead and the promise that neighbourly relations hold" for the people of both countries, Krishna said.
No date was scheduled for future meetings.
Krishna is the highest level Indian official to visit Pakistan since November 2008, when fighters attacked Mumbai, India's financial capital, leaving 166 dead.
India blamed Pakistan-based fighters for the attacks.
Ahead of talks, G K Pillai, India's home secretary, blamed Pakistan's Inter-Services Intelligence agency (ISI) for orchestrating the Mumbai attacks.
Pillai said information on ISI involvement emerged from the interrogation of David Coleman Headley, an American who pleaded guilty in US courts to helping organise the attacks.
Krishna said he would return to New Delhi "with an assurance from the highest level" of Pakistan's political leadership over leads got by the interrogation of Headley.
"I'm going back with the hope there will be further interrogation based on leads given by Headley," he said.
"If it could help unravel the conspiracy and go after the perpetrators of the Mumbai attacks, there could be the biggest confidence-building measure."
The ISI has denied any involvement with the Mumbai attacks.
Some of the more intense moments at the press conference came when ministers were asked about India's alleged backing of ethnic Baluch insurgents in Pakistan's Baluchistan province.
|Shah Memood Qureshi says Pakistan has not been supporting attacks against India [Reuters]
Krishna insisted that Pakistan had not provided any evidence about its claims against India on the Baluch issue.
He added that India saw a 40 per cent increase in militant infiltration from Pakistan into Indian-held Kashmir between 2008 and 2009.
Quershi retorted that "inflitration is not the policy of the government of Pakistan or any intelligence agency of Pakistan, period. If there are individuals who have crossed over, deal with them firmly and Pakistan will cooperate."
"India and Pakistan, both are victims of terrorism, the best way to deal with this challenge is to recognise this as a common enemy and adopt a common approach vis-a-vis this menace," Quershi said.
The US is pushing India and Pakistan to resolve their differences, in part because it wants Pakistan to move troops away from Kashmir and into the border regions with Afghanistan where the Taliban are gaining strength.