"All my colleagues and the public should be aware that I, as public prosecutor, have been prevented from launching an investigation," Muammer Akkas said in a statement.
A high-level bribery and corruption investigation ensnaring former ministers and top businessmen prompted a cabinet reshuffle Wednesday by Prime Minister Recep Tayyip Erdogan after three ministers stepped down.
Despite the reshuffle and resignations, Erdogan is seen as defiant in the face of the graft allegations, which he claims are being advanced by a shadowy international cabal. He has already ordered the sacking of dozens of police officers involved in the probe.
But many observers see the developments as a blow to his 11-year reign, during which he has built a reputation as a formidable economic steward but an autocratic leader.
The prosecutor's statement comes a day after Akkas reportedly ordered the detention of 30 more suspects including ruling party lawmakers and businessmen.
"Despite a meeting with the (Istanbul) police chiefs who would oversee the operation at the court building, I found out that the court order and the detention decision had not been implemented," Akkas said.
The prosecutor said the judiciary was subjected to "clear pressure from both the (Istanbul) chief prosecutor's office, and the justice police who are entitled to obey court orders".
Akkas also claimed that the police chiefs committed an offence by disobeying the court orders, which he said paved the way for suspects to "take precautions, flee and black out (get rid of) evidence".
Istanbul chief public prosecutor Turan Colakkadi, at the centre of Akkas's criticism, hit back at the charges and said that prosecutors were not mandated to launch "random investigations".
Colakkadi also claimed the prosecutor was removed from the investigation because he had mishandled the proceedings and had leaked information to the media.
Turkey's Higher Board of Judges and Prosecutors however backed the prosecutor and said police were responsible for obeying orders from him.
"In case of illegal actions, judicial checks on (the country's) rulers are an essential part of the democratic state governed by rule of law," it added.
Akkas meanwhile also said that the probe into the alleged corruption had been taken away from him.
Political observers have linked the bribery probe to tensions between Erdogan's government and followers of the influential Muslim cleric Fethullah Gulen, whose followers hold key positions in the police and judiciary.
The Turkish premier says he is fighting against a "state within a state", widely seen as a reference to the influential Gulenist movement, a key backer of his government when he first came to power in 2002.
The scandal that erupted in the run up to Turkey's local elections in March are posing the most serious threat to Erdogan's grip on power. His image was already bruised by a wave of anti-government protests in June.
