The military, which has ousted four governments in the past 50 years, had been seen as virtually untouchable and the appearance of high-ranking officers in a civilian court would have been unthinkable only a few years ago.
The officers were released after 10 hours of questioning by prosecutors over what they knew about a plot to oust the ruling AK Party of Prime Minister Tayyip Erdoğan.
İstanbul Deputy Chief Prosecutor Turan Çolakkadı said after the testimony that the commanders were treated as suspects.
What they said may have serious political ramifications if it implicates top brass and if their testimony is leaked. That could bring the armed forces closer to a confrontation with Erdoğan's government.
About 200 people, including military officers and politicians, are already standing trial over their alleged part in the Ergenekon, a clandestine criminal organization accused of plotting to topple the AK Party government.
Turkish financial markets have suffered several bouts of jitters since the Ergenekon affair first surfaced in 2007. Turkey is bidding to join the European Union and EU officials are closely following the case to see how its democratic institutions stand up to the test.
The military says no one in its ranks had plans to topple the government.
The commanders were expected to have responded to testimony given earlier by a former military chief of staff.
While his evidence had been conducted in camera, the chief later said in newspapers that he had told the prosecutors he had known of the existence of plans to topple the government.
Media outlets have also published alleged excerpts of a diary of former Naval Commander Özden Örnek from 2004, which referred to the coup.
Örnek was one of the three commanders called to give testimony on Saturday. He served as Naval Commander from 2003 to 2005.
Also being questioned were former Land Forces Commander Aytaç Yalman, who served from 2002 to 2004 and former Air Force Commander İbrahim Fırtına who served from 2003 to 2005.
A navy colonel and lieutenant were arrested after being questioned in the same courthouse on Saturday. Their arrests were also under the umbrella of the Ergenekon investigation, but they were implicated in a separate plot, police said.
Two retired generals have already been arrested in the Ergenekon investigation and are being tried.
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