The arrest was the latest in a long-running investigation of what prosecutors say was a plot hatched by members of the military to attack and kill Christians and other minorities and blame Islamists in order to discredit the government.
Col. Levent Gülmen was arrested in the seaside town of Foça while attending ceremonies marking a national holiday.
He had been detained once before and released, in 2010, Sabah newspaper quoted his lawyer as saying. The lawyer, Murat Ergün, called Saturday's detention a "bureaucratic mistake." The court didn't register that the arrest warrant earlier issued was dropped.
Media reports about the Cage Action Plan first surfaced in late 2009.
The plot is linked to the wider Ergenekon probe, in which hundreds of retired and serving members of the military, academics, journalists and lawyers have been detained on suspicion of being part of several conspiracies to push Prime Minister Recep Tayyip Erdoğan from power.
The trials have reined in the influence of the military, which had appointed itself guardian of Turkish secularism and ousted four governments since 1960.