The conference discussed measures to promote reconciliation
Afghan President Hamid Karzai has ordered a review of the cases of every Taliban suspect in the country's prisons.
He said that where evidence against suspects was doubtful, they must be released.
Meanwhile, Mr Karzai's office says Interior Minister Hanif Atmar and intelligence chief Amrullah Saleh have resigned.
It said they quit over the attack on last week's national peace conference.
The statement said the explanations they gave the president for last week's attack by the Taliban on the peace jirga was "not satisfactory", and Mr Karzai had accepted their resignations.
None of the delegates were hurt in the Taliban assault, which saw rockets fired at the Kabul venue.
Mr Karzai's announcement of prisoner case reviews is the first official response to the national peace conference, which ended on Friday.
The conference discussed measures to promote reconciliation, including negotiations with militant factions, and recommended the release of Taliban suspects being held in Afghan police custody and by the US military if they were being held on "inaccurate statements or unsubstantiated allegations".
It is unclear how many people the review will affect. Hundreds of prisoners are accused of Taliban involvement.
A committee will be set up to oversee the investigation of each case.
Meanwhile, Nato says five international troops have been killed in three separate incidents in Afghanistan on Sunday.
The Western military alliance said three members of its force were killed in a vehicle accident in southern Afghanistan.
Another soldier died in a bomb explosion in the south, while a fifth was killed in an insurgent attack in eastern Afghanistan.
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