Hussein Abdel Ghani was accused of broadcasting false information liable to harm Egypt's reputation, Aljazeera said on Thursday as fellow journalists condemned the arrest as an attack on the freedom of the press.
On Wednesday, Aljazeera reported that Abdel Ghani disappeared in the Sinai peninsula where he had gone to follow up on Monday's deadly explosions in the Dahab resort and the two suicide bombings which occurred on Wednesday elsewhere in Sinai.
Two men in civilian clothes had asked to speak to him in private shortly before his disappearance, Aljazeera said.
His whereabouts remained unknown but Aljazeera said it had learned through private sources that he was being interrogated for purportedly spreading false news.
Aljazeera reported on Wednesday that an attack had targeted policemen in the town of Belbeis, northeast of Cairo.
Other media said a police station had been fired on, quoting witnesses and security sources, but the Interior Ministry later issued a denial, which Aljazeera also carried.
Officials of the Egyptian journalists' trade union went to assist at Abdel Ghani's interrogation by prosecutors of the state security court after he was brought to Cairo from Dahab.
One of them, Gamal Fahmy, told AFP: "We consider the arrest of the head of the Aljazeera bureau to be an attack on press freedom in Egypt.
"For years the journalists' union has been demanding the abolition of laws restricting press freedom, including the legislation under which Mr Abdel Ghani faces prosecution."