The meeting in Islamabad began after both sides failed to meet Tuesday as originally scheduled due to questions over the composition of the negotiating team representing the outlawed Tehreek-e-Taliban Pakistan.
At their first meeting, both sides expressed their resolve to keep talking despite the ongoing violence and agreed that neither side would issue statements against the other, the state-run Associated Press of Pakistan reported.
At a news conference, Irafan Siddiqui, leading the government side, and Maulana Samiul Haq, speaking for the TTP, also said they do not want the talks to drag on for a long time, the news agency said.
Dawn newspaper said the peace talks, called by Pakistani Prime Minister Nawaz Sharif's government, were being held despite much skepticism whether they will produce lasting peace after about seven years of bloody insurgency by militants.
Thursday's meeting lasted about 4 hours, Dawn said.
A joint news release said the government side stressed the talks be held within the framework of the constitution, and that the scope of the peace talks be limited to only insurgency-affected areas. The government also said all activities that may negatively affect the peace efforts should immediately cease.
The TTP side urged the government to clarify the mandate and level of authority of its four-member committee, and its ability to implement a peace pact.
Besides Siddiqui, a special assistant to the prime minister, other government negotiators are Rustam Shah Mohmand, former ambassador to Afghanistan, journalist Rahimullah Yousufzai and retired Maj. Amir Khan.
In addition to Maulana Haq, the TTP side was represented by Maulana Abdul Aziz and Mohammad Ibrahim. Two more negotiators nominated from two political parties declined to be on the team.
TTP spokesman Shahidullah Shahid was later quoted as saying the three-member committee was final and that "we have our full confidence in it to hold talks," Dawn reported.
Sharif, who announced the talks last week, has said he was optimistic there would be a positive outcome.
The TTP has stepped up its violence since its leader, Hakimullah Mehsud, was killed in a drone strike last November. Earlier peace talk offers had been spurned.
The violence in the past seven years has killed hundreds of people, including Pakistani security personnel.
In announcing the talks last week, Sharif, who became prime minister after elections last May, said his government is keen to give them a last chance to save the country from terrorism. He also said his government will not allow the country to be held hostage by them.
Prior to the offer to negotiate, there had been rumors the government was considering a major military offensive against the militants.
Earlier, some analysts told the New York Times Pakistan's powerful military, under their new chief, favors using force against the militants.
Hasan Askari Rizvi, a prominent Pakistani academic, told the Times the Taliban has shown shrewdness in picking mainstream religious leaders to represent them at the talks.
"If the talks eventually fail, which is highly likely, [Sharif] will be left with no option but to support a military action," Rizvi told the Times. "If he does not, then there will be a serious civil-military crisis."
In other developments, a Pakistani Foreign Office spokeswoman in her media briefing said the peace talks are an internal matter and described as hypothetical a question about whether Pakistan would sever its alliance with the United States in the war on terror if the TTP made it a condition for the peace talks.