The Beersheba Magistrate's Court said the Shin Bet security service and police arrested Wael Abu Reda, 35 years old, on suspicion of having committed "security crimes."
No details of the alleged offenses were made available. The court extended the suspect's remand by eight days.
The confirmation of Abu Reda's arrest comes three weeks after he had mysteriously disappeared from the Egyptian side of Rafah, a town on the Gaza-Sinai border where he was due to meet a friend. Prior to his disappearance, he arrived at a town near Cairo to seek medical treatment for his son.
Abu Reda's wife, Amani, told foreign media at the time she was "clueless" with regard to the circumstances of his disappearance. Relatives said they were not aware of any ties he may have had with Gaza militants.
Israel's Public Defender's Office said it had been assigned Abu Rida's case on June 22 and appointed him a lawyer.
It remained unclear how Abu Rida, who previously worked as a policeman for the Palestinian Authority in Gaza, ended up in Israel.