Some 52 people - including three sons of cabinet ministers - were arrested in dawn raids on Tuesday in connection with a high-profile bribery inquiry.
Five police chiefs who oversaw raids in Istanbul and Ankara were sacked for "abuse of office", Mr Erdogan said.
"We will not allow political plotting," the prime minister said.
However, the deputy prime minister promised not to stand in the way of the judicial process.
"We will always respect any decision made by the judiciary and will not engage in any effort to block this process," Bulent Arinc said.
Commentators in Turkey believe the arrests - and subsequent firings - are evidence of a new dramatic fault-line in Turkish politics, one within the AK Party itself, the BBC's James Reynolds reports.
The feud is believed to involve supporters of Fethullah Gulen, an influential Islamic scholar living in self-imposed exile in the US who once backed the ruling AK Party, helping it to victory in three elections since 2002.
Members of Mr Gulen's Hizmet movement are said to hold influential positions in institutions such as the police, the judiciary and the AK Party itself.
In recent months, the alliance began to come apart and in November the government discussed closing down private schools, including those run by Hizmet.
Mr Gulen has been living in the US since 1999, when he was accused in Turkey of plotting against the secular state.
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