By Jonathon Burch
ANKARA (Reuters) - Turkey's number-two naval commander retired on Monday in what some took as proof of deepening frustration in the military high command over the jailing of hundreds of their colleagues.
Prime Minister Tayyip Erdogan's administration has detained several hundred serving and retired officers over the past few years, including one fifth of Turkey's military generals, on charges of conspiring to overthrow the government.
Vatan newspaper quoted Admiral Nusret Guner, who was operational commander of the navy, as saying: "Our friends are being imprisoned one by one and we are not able to do anything; in fact, we are even helping them to be jailed".
During his 10 years in power, Erdogan has brought the once-supreme armed forces to heel with reforms designed to stop them interfering in politics.
More than 300 past and present officers were convicted and handed lengthy prison sentences last September for plotting to topple Erdogan's administration almost a decade ago.
Newspapers reported over the past week that Guner, who is in his early sixties, had tried to resign after the convictions.
Daily paper Sozcu, a fierce critic of Erdogan's government, quoted Guner's wife on Friday as saying he had met Erdogan previously on the issue and traveled to Ankara last week for more meetings, handing in his resignation letter on Wednesday.
Turkey's military rarely talks to the media and Reuters could not independently verify the reports.
In a statement on Monday confirming Guner's departure, the military general staff did not give a reason for the decision. "The retirement request of our navy commander which has appeared in media outlets in recent days has been accepted," it said.
Erdogan, whose ruling party has moderate Islamist roots, has received praise at home and abroad for bringing the military, which sees itself as the guardian of secularism, under civilian control.
The years that defendants have spent in prison without conviction, however, have raised fears that the conspiracy trials are a political witch hunt aimed at silencing opposition.
Around 100 journalists are also in prison, as well as thousands of activists, lawyers, politicians and others. Most are accused of plotting against the government or supporting outlawed Kurdish militants.
As public support for the investigations dwindles, with critics and even sympathizers saying the number of military officers charged with sedition has spiraled out of control, Erdogan has moved to distance himself from the trials.
On Friday he criticized the lengthy pre-trial detentions, suggesting they were sapping the army's morale and affecting its ability to fight a Kurdish insurgency.
Last July, parliament voted to abolish special courts used in coup conspiracy cases after Erdogan criticized prosecutors for acting as if they were "a different power within the state".
But the end of the special courts, established by Erdogan's government in 2005, will not affect existing prosecutions of the hundreds of military officers already in jail.
The most defining moment that underlined Erdogan's grip over the armed forces came in July 2011, when the chief of general staff and his top three commanders quit in protest at the detention of 250 officers on conspiracy charges.
The country's top military officer was then replaced with a general seen as less outspoken and who has largely stayed out of the public eye. Guner was expected to have taken over the top naval role this August when the current admiral steps down.
Media have reported there are now no admirals in the navy to take over the top role, meaning another officer would need to be promoted by August 30 when the commander of naval forces retires.
(Editing by Tom Pfeiffer)