Police reportedly searched the Gulhane Military Medical Academy (GATA) hospital in the capital.
Turkey on Tuesday issued arrest warrants for 100 staff, including doctors, at the main military hospital in Ankara as part of an investigation into last month's failed coup, a Turkish official and reports said.
Police were searching the Gulhane Military Medical Academy (GATA) hospital in the capital, the private NTV television reported. It was not immediately clear if any suspects had been detained.
The Turkish official, speaking on condition of anonymity, confirmed that detention warrants had been issued without giving any number.
Turkey blames the coup attempt on the organisation of US-based Islamic cleric Fethullah Gulen, who Ankara accuses of running a group called Fethullah Terror Organisation (FETO), charges he denied.
The official said that staff at the hospital were suspected of helping fast-track Gulen supporters into the military by giving them favourable medical reports.
"GATA is crucial because this is where fitness and health reports are issued," the official said.
"There is strong evidence suggesting FETO members infiltrated this institution to slow down the career progress of their rivals within the military and fast-track their supporters."
Similar claims have also been made about military schools where officials have said exams were rigged. Almost half of Turkey's generals were fired in the wake of the coup.
Turkey has declared a state of emergency in the wake of the July 15 power grab attempt and launched a crackdown that has seen some 18,000 people detained.
This is believed to be the first time a medical establishment has been targeted in the clampdown, which has also hit journalists and academics.
Under a previous decree, GATA and other military hospitals have been transferred to the control of the health ministry.