Last October, an appeals court ordered a retrial of 88 people, including former army chiefs, who had been sentenced to prison terms of up to 20 years.
The criminal court in Istanbul acquitted a total of 25 defendants, citing a lack of tangible, credible evidence against them, and decided to review the dossiers of the remaining suspects, the private Dogan news agency said.
Those acquitted were largely mid-ranking former army officials but also included Omer Faruk Yarman, the former CEO of Turkish defence and software manufacturer Havelsan.
In a separate development in the case, magistrates in Istanbul had on Thursday ordered the release of 230 military officers after Turkey's top court said the original trial was flawed.
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Turkey's once-powerful army, which considers itself the self-appointed guardian of secular rule, has staged three coups since 1960 and forced out an Islamic government in 1997.
Erdogan has spent the best part of his 11 years in power trying to curb the military's influence through a series of trials, which have long been criticised by rights groups questioning their impartiality.
In a gesture towards the army, parliament in February abolished specially appointed courts that convicted dozens of army officers, paving the way for retrials.