Kenan Ipek, Justice Minister and Chairman of the Supreme Board of Judges and Prosecutors, or HSYK, said in a written statement on Tuesday that an office of the board had opened a file and ruled an inspector should investigate the claims.
The Turkish government has long held that a "parallel state" of Turkish bureaucrats and senior officials are embedded in the country's institutions, including the judiciary and the police, and plotting to undermine it.
Ipek said the move came amid claims judges and public prosecutors had "established a parallel judicial power as offsets of the terrorist organization called the parallel state, which has its own organization and hierarchical structure in the Turkish judiciary, (and) is acting in an organized way as an alternative to the state judiciary".
The statement described the "parallel state" as an "organization that targets those who dissent with it, implements the decisions taken by the senior executives of the organization upon intelligence gathered via the police department and the judiciary, and behaves unjustly toward several people by using the judiciary power, regardless of their innocence".
Istanbul Chief Public Prosecutor Hadi Salihoglu also announced on Tuesday 24 suspects had been taken into custody in an Istanbul-based operation launched early on Monday across Turkey, in an ongoing "parallel state" probe.
Salihoglu said in a written statement that five other suspects are still at large and arrest warrants had been issued for 29 suspects on charges of "forming a criminal organization, wiretapping espionage, violation of privacy, storing personal data in violation of the law, forgery of official documents".
The detainees include the former vice-head of the Istanbul Security Department and chief of Istanbul Organized Crime Control Bureau.
The government alleges the clandestine "parallel state" network is run by U.S.-based preacher Fetullah Gulen and that his so-called Gulen movement is responsible for masterminding a plot to overthrow the elected Turkish government.
Fethullah Gülen, the leader of the worldwide Gülenist crime network who has been living for years under the protection of the US government on a ranch in Pennsylvania, has been alleged to have established an illegal network within the Turkish state.
Turkey wants Gulen to be extradited from the U.S., where he has lived since 1999.
An Istanbul criminal court has issued an arrest warrant for Gulen as part of a probe into the parallel state operation.