Judges Metin Ozcelik and Mustafa Baser at the weekend issued an order to release the 74 former police and the head of the Samanyolu TV channel Hidayet Karaca from police custody.
All are accused of being allies of Erdogan's arch foe, the US-based preacher Fethullah Gulen, and working with him in a parallel state aimed at overthrowing the government.
The decision had been blocked by a higher court and the judges themselves were then suspended by Turkey's Supreme Board of Judges and Prosecutors (HSYK).
Ozcelik was arrested late yesterday and was remanded in custody in Silviri prison on the outskirts of Istanbul.
Also Read
Baser meanwhile surrendered to the authorities at the Bakirkoy court in Istanbul this morning, Anatolia said.
NTV said Baser was remanded in custody by the court after a lengthy hearing.
Both have been charged with membership of an armed group and impeding the work of the government, it added.
Gulen leads a broad movement known as "Hizmet" (Service), believed to be supported by millions of Turks and which brings together interests ranging from finance to schools to media.
Gulen, who left for the US in 1999 to escape charges of anti-secular activities by the government at the time, has denied being behind the graft allegations against Erdogan.
The 75 suspects were never released and remain in detention.
They had all been detained in a series of raids that started last year against supporters of Gulen in the Turkish security forces.
Karaca leads a strongly pro-Gulen television channel and his arrest had been condemned by media rights groups.