EU Affairs Minister Ali Haydar Konca and Development Minister Muslum Dogan said the state's two-month-old offensive against the militant Kurdistan Workers Party (PKK) had created a "hellish" situation "especially in the Kurdish cities".
"A logic of war has been put into place," Konca, a member of the pro-Kurdish Peoples' Democracy Party (HDP), told a press conference, describing the climate in the country as worse than during the height of the conflict between the state and the rebels in the 1990s.
NTV channel reported that the pair -- who have been vocal critics of the AKP -- walked out over a debate on terrorism during a cabinet meeting.
A statement from Prime Minister Ahmet Davutoglu's office said he had accepted the resignations and that neither would be immediately replaced, NTV reported.
Deputy Prime Minister Numan Kurtulmus condemned the departing ministers' criticism of the government and president as "unacceptable."