The committee quit in protest at a military raid in North Waziristan that they said violated the accord.
The resignations came days after the military said it had attacked a training camp near the Afghan border on Tuesday, killing four suspected fighters.
Security forces, backed by helicopter gunships, attacked the suspected base near Miran Shah after people inside opened fire at tribal elders sent to persuade them to surrender, the military said.
But the committee claimed civilians were killed in the attack, and that it was carried out without their approval.
The government signed the deal to stop attacks by pro-Taliban fighters on its security forces inside Pakistan and Afghanistan and to expel foreign fighters.
In return, local fighters had been given amnesty.