There has been a history of tension between the secularist military and the governing AK party, with the two sides engaged in a war of words for the past two years over allegations that parts of the military had been plotting a coup.
Investigations into those allegations, known as the "Sledgehammer" conspiracy - appear to be the root cause of today's resignations, says the BBC's correspondent in Istanbul, with the senior military wanting to go ahead with scheduled annual promotions for some of the officers implicated - and the government refusing.
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