Hasan Hami Yildirim had criticised the government for exerting pressure on the judiciary over the graft investigation, which has plunged Turkey into political turmoil just three months ahead of key elections.
A string of public figures including high-profile businessmen and the sons of three ministers were detained on December 17 over allegations of bribery for construction projects as well as illicit money transfers to sanctions-hit Iran.
Five MPs including a former culture minister have resigned from the AKP since the raids, which the government has suggested were instigated by supporters of an influential US-based Turkish cleric.
The corruption scandal has exposed a seething feud between the ruling Justice and Development Party (AKP) and a former ally, influential Muslim cleric Fethullah Gulen, whose supporters hold key positions in the police and the judiciary.
The latest resignation has reduced the number of AKP seats in parliament to 320 out of 550.
The government is set for a key test in March local elections, which will be followed by an August presidential vote and parliamentary elections in 2015.
"I wish that the views and opinions I expressed were taken into consideration but I saw that if I stayed in the party I would have been subject to more criticism and I could not take that."
Yildirim had previously criticised the removal from the probe of Istanbul prosecutor Muammer Akkas who had been set to order a second wave of arrests, reportedly including Erdogan's son.
"Pressure on prosecutor Muammer Akkas is unacceptable. This pressure cannot be legitimised in a state governed by rule of law," Yildirim said on Twitter.
Government spokesman Bulent Arinc announced yesterday that plans were in the making for legal action against judges and prosecutors accused of wrongdoing or abuse of power.
Erdogan's government has already ordered the sacking of dozens of police chiefs linked to Gulen or who oversaw the December 17 raids, including the powerful head of the Istanbul force.
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