Brigadier air force general Bekir Ercan Van was detained along with 11 lower-ranking officers on Saturday at the air force base of Incirlik in Turkey's southern Adana province, the official said.
One police officer from the base was also arrested. All are suspected of "complicity" in the coup plot, the official said.
Officials have said the authorities suspect that Incirlik was used by rogue troops to refuel military aircraft "hijacked" by the coup plotters on Friday night.
The US said today that strikes had resumed from the base, after Turkish authorities imposed a security lockdown in the wake of the coup attempt, allowing no movement in or out.
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"As a result, counter-ISIL coalition air operations at all air bases in Turkey have resumed," he added, using an acronym for the IS group.
"Turkey suspects a small group of Turkish troops stationed at Incirlik supported the coup attempt," said the official.
The official added the air space closure was a short-term measure that "won't have a significant impact on coalition operations" against IS.
French Foreign Minister Jean-Marc Ayrault said the events of the past two days had raised questions about Turkey's "reliability" in the fight against IS.
"There's (the question of) reliability on the one hand and, indeed, an element of suspicion on the other," he told France 3 television.