“The Istanbul court has now overturned its own release verdict … Taner will stay in pre-trial detention,” Turkey’s Amnesty researcher Andrew Gardner said on Twitter.
“This is devastating for Taner’s family and a disgrace to justice,” he added.
Kilic has been held since June 2017 in the western city of Izmir, accused of links to US-based preacher Fethullah Gulen who Turkey says ordered the July 2016 coup bid.
Amnesty has denounced the allegations against Kilik as “baseless”.
Gulen and his followers meanwhile deny any links to the coup, and reject the Turkish government’s attempt to label them as a terrorist group.
The Istanbul court had on Wednesday ordered his release on judicial control, to the delight and relief of his family and friends.
But their joy was sapped hours later after he was taken back into custody straight after his release.
It later emerged that the prosecutor had appealed the decision to release him on Wednesday, while a second court ordered his continued detention and issued an arrest warrant, Gardner told AFP.
Then on Thursday the first court reversed its own decision, he added.
“The court changed its mind. Why? Who knows, no grounds provided. Devastating for the family and an affront to justice,” Amnesty’s Europe director Gauri van Gulik said on Twitter.
Authorities accused Kilic of having an encrypted messaging application on his phone in August 2014 called ByLock, which Ankara claims was especially created for Gulen supporters.
But Kilic has vehemently denied he ever had the app.
He is on trial with 10 other rights activists including Amnesty’s Turkey director Idil Eser, German activist Peter Steudtner and Swedish colleague Ali Gharavi.
The other 10 were all released last year though their trial continues, with the next hearing set for June 21.
The 10 are accused of links to Gulen and other outlawed groups including the Kurdistan Workers’ Party (PKK), which has waged a three-decade insurgency against Turkey.
Download our app and read this and other great stories on the move. Available for Android and iOS.