Turkey's top military brass resigned on Friday, in the latest and possibly decisive round of a long battle between the traditional secularist establishment embodied by the army and the Islam-rooted government of Tayyip Erdogan that has dominated Turkey for nearly a decade.

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The head of Turkey's military quit on Friday along with the army, navy and air-force chiefs in protest against what he called the unjust detention of 250 military officers held on charges of conspiracy against Prime Minister Erdogan's government.

It lays open the deep rift between a military badged with the legacy of Mustafa Kemal Atatruk, founder of the Turkish Republic, and a rival elite represented by Erdogan's Justice and Development Party (AK), with Islamist roots and a vast following in the conservative heartland of Anatolia.

State-run Anatolian news agency said the head of the armed forces General Isik Kosaner and the commanders of the ground, naval and air forces had requested retirement. Some Turkish media initially reported they had resigned.

Kosaner in a farewell message to comrades, reported by Anatolian, made clear he was leaving in protest against a flawed judicial process that has led to the detention of officers caught up in a coup conspiracy case.

"It has become impossible for me to continue in this high office because I am unable to fulfill my responsibility to protect the rights of my personnel as the Chief of General Staff," Kosaner said.

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Some 250 military personnel are currently detained in jail, including 173 serving and 77 retired personnel. Most of them on charges related to an alleged plot in 2003, known as "Operation Sledgehammer".

"As many jurists have said, it is impossible to accept their detention as being in line with principles of universal law, justice and moral values," Kosaner said.

More than 40 serving generals, almost a tenth of Turkey's commanders, are under arrest, accused of a series of convoluted conspiracies to bring down the AK party.

While the Erdogan government is admired at home and abroad for bringing the military under civilian control, the length of time it is taking to bring those accused to trial, and the widening net dragging in more alleged conspirators, is setting off alarm bells.

A prosecutor investigating another alleged plot involving military officers on Friday sought the arrest of 22 people including the commander of the Aegean army, media reports said.

Erdogan's office made no reference to the commanders' reasons for retiring in a statement issued later that named General Necdet Ozel, commander of the paramilitary Gendarmerie, as the new land forces chief, and deputy chief of general staff.

"Our Turkish Armed Forces, one of the biggest and most respected in the world, will continue... to do their duty given by laws successfully in a spirit of unity and togetherness," the statement said.

It went on to say that the Supreme Military Council will meet as planned on Monday for a twice yearly meeting to begin deciding key appointments.