Gul said Turkey has experienced deep judiciary reforms, and "should a country where such (reforms) have been made witness corruption, it would not and cannot be covered up."
The anti-corruption that began last week brought about the incarceration of two dozens of bureaucrats and businessmen, including the sons of two key cabinet ministers and the head of state-owned lender Halkbank.
Top leaders and senior officials from the ruling Justice and Development Party have voiced concern that the operation was intended to go beyond its judicial mandate and harm the Turkish government and economy.
During a ceremony of presidential awards in culture and arts, President Gul touched on the recent debate of a "parallel state" within the state, saying "no authority or solidarity can exist" other than that of state institutions under the constitution and law.
"Turkey is not the same country as it was 15-20 years ago. There have been extraordinary reforms in the last decade. Laws, everything. So everyone should be confident on this," Gul said.
President Gul said he believed the judicial process would go as smoothly as it should and help bring out the truth.
He noted that the important thing was "to become aware of mistakes and deficiencies in our immediate surroundings and be determined to redress them."