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The insurgents have been battling to topple Pakistan's government and establish strict Islamic rule since 2007, but Prime Minister Nawaz Sharif believes both sides are now ready to find a negotiated settlement and stop fighting.
In a statement after the meeting, which lasted over three hours, the two sides stressed their commitment to dialogue.
"Both committees concluded that all sides should refrain from any act that could damage the talks," it said. "Both condemn recent acts of violence in Pakistan, saying such efforts should not sabotage the talks."
Irfan Siddiqui, a government negotiator picked by Sharif, sent a text message from the meeting in an Islamabad government building, describing the atmosphere as "cordial and friendly".
Several earlier efforts at striking peace deals with the militants failed to end the violence for long, only allowing them to regroup, recruit new fighters and strike back with renewed vengeance.
Pakistan's neighbours are watching closely, acutely aware that another failure to find a peaceful solution could further destabilise the region already nervous ahead of the expected pull-out of most foreign forces from neighbouring Afghanistan.
Thursday's meeting in Islamabad was a preliminary round where the two sides were expected to agree on a broad roadmap for future contacts.
But many in Pakistan doubt that talking to an insurgent group that stages almost daily attacks will succeed.
As the sides prepared for talks this week, a suicide bomber killed eight people near a Shi'ite Muslim mosque in the city of Peshawar. The Taliban have tried to distance themselves from the attack but the bombing reinforced doubts about the talks.
Taliban bosses watched the progress of the talks in Islamabad from their mountainous hideouts on the Afghan border, with their interests represented by three Taliban-friendly public figures hand-picked by the insurgents.
"The progress of the talks will be submitted to the prime minister," said a government official, who declined to be identified, as he was not authorised to comment on the talks.
The Pakistani Taliban, known as Pakistani Tehreek-e-Taliban, are a deeply fragmented umbrella group consisting of dozens of entities, so striking a deal with one of them would not necessarily stop the violence.
On Tuesday, the first attempt at talking got off to a shambolic start after government negotiators failed to turn up at an agreed time, angering the insurgents' representatives.
"The unavoidable question for the government though: what are talks meant to achieve if violence continues even in the immediate run-up to the first real, known attempt at talks?" the respected Dawn daily wrote in an editorial.
Militants have stepped up attacks against security forces since the beginning of the year, prompting the army to send fighter jets to bomb their strongholds in the ethnic Pashtun region of North Waziristan, along the Afghan border, and triggering talk that a major ground offensive was in the works.