According to a statement from the prime minister’s office quoted by NTV, Prime Minister Ahmet Davutoglu accepted their resignation, and neither will be immediately replaced in his cabinet.
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Ankara has intensified its military campaign against the Kurdistan Workers party (PKK) in the past few months.
Violence between the PKK and Turkey’s military reignited this summer after the collapse of a tentative peace process.
Erdogan has repeatedly accused the HDP of being a front for the PKK, which is blamed for a string of bomb and shooting attacks that have killed dozens of soldiers and police in the majority Kurdish southeast in recent weeks. The HDP, however, has succeeded in widening its support base, bringing in non-Kurds opposed to Erdogan and disillusioned with the main opposition Republican People’s Party (CHP).
The HDP, which grew out of the Kurdish nationalist movement, won an unusually high share of the vote in last June’s election after broadening its appeal to attract leftist and liberal votes from across Turkey.
Davutoglu formed a caretaker government once coalition negotiations failed and Erdogan called new elections in November.
Two ministers from the pro-Kurdish Peoples’ Democracy Party (HDP) have resigned from Turkey’s interim government.
But polls show the AKP still struggling to win back voters.
Concerns over the ruling party’s approval rating come as Turkey has been under pressure over its decision in June to start attacking purported Daesh militant positions in Syria.
A survey by Gezici polling company published Monday showed support for the party slipping 1.6 points since June, dropping from 40.9 to 39.3 percent.
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His critics accuse him of using a suicide bombing in a southeastern Turkish town that was blamed on ISIL extremists as a pretext for reigniting a three-decade conflict with the PKK for electoral gain. The group, its fighters concentrated across the border in the mountains of northern Iraq, says it now seeks greater Kurdish autonomy.
