The affair comes on the eve of a key visit by US Secretary of State Rex Tillerson.
But the US embassy in Turkey said its Istanbul consulate contacted theology lecturer Adil Oksuz only to inform him that his American visa had been revoked.
The affair comes on the eve of a key visit by US Secretary of State Rex Tillerson who is due to meet in Ankara with Turkish leaders including President Recep Tayyip Erdogan.
Turkish officials have said that Oksuz was the so-called "imam" of the plot and in charge of coordinating between US-based preacher Fethullah Gulen and the army before the July 15 failed coup.
Gulen is accused by Ankara of ordering the attempted putsch aimed at overthrowing President Recep Tayyip Erdogan. He strongly denies the charges.
Oksuz was detained in the aftermath of the coup but then released and is now on the run.
The embassy in Ankara said the US consulate general in Istanbul called Oksuz on July 21 after Turkish police contacted the US mission in Turkey the same day for help in preventing him leaving the country.
"We then revoked his US visa and, as required by US law, tried to call him to inform him of the cancellation," the embassy said in a statement.
It was responding to Turkish media reports quoting the Ankara prosecutor who said a phone number belonging to the consulate called Oksuz, mentioned in an indictment against him on Wednesday.
Turkish Prime Minister Binali Yildirim said that the US statement was not enough.
"That is the official statement if you buy it," he told the private NTV television late on Wednesday.
"We need to check whether or not there are other things… We expect more satisfactory response," he said.
The US embassy insisted that "far from being suspicious, the call from the consulate general illustrates the close US-Turkish law enforcement cooperation following the coup attempt".
Last July, pro-government local media speculated over whether the US was involved in the coup, including Yeni Safak daily columnist Ibrahim Karagul who claimed the US wanted to kill Erdogan.
In the weeks after the failed coup, American ambassador to Ankara John Bass was forced to say the US did not "plan, direct, support or have any advance knowledge of any of the illegal activities" on July 15.