Turkish President Abdullah Gul said on Friday no parallel formations could be allowed to exist within the state, referring to allegations a "parallel state" nestled in judiciary and police is plotting against the Turkish government, Anadolu Agency reported.
A comprehensive graft probe launched on December 17 caused controversy after it led to high-profile arrests.
In a televised interview, President Gul said the priority was to ensure graft claims are thoroughly investigated.
"Courts should act according to the constitution, laws and regulations. They should guard themselves against any other reason or motivation, be it ideological, religious, or political."
Prime Minister Recep Tayyip Erdogan earlier said the probe was a "dirty setup" with international links designed to hinder Turkey's economic advance.
Turkey's sole exchange entity has lost close to ten percent since the operation, with the total loss of value estimated at upwards of 50 billion dollars.
"Economic stability comes first. Turkey is a globalized economy," Gul said. "If expectations turn to despair, we would be drilling holes in our own ship."