The suspect, who was arrested on Monday just hours after the attack, appeared before a court in Kfar Saba near Tel Aviv where his remand in custody was extended until October 11, police spokesman Micky Rosenfeld said, without giving details about his identity.
Widespread reports in the Israeli media said the suspect was an 18-year-old Jewish youth from the Galilee region, who was arrested in the West Bank where he attends a Jewish seminary.
The attack, which took place before dawn on Monday, saw an unknown number of attackers set light to the mosque in the Bedouin town of Tuba Zangaria, 10 kilometres (six miles) north of the Sea of Galilee, causing heavy fire damage and destroying Muslim holy books.
The perpetrators also scrawled the words "tag" and "revenge" on the walls, in what police described as "a very severe price tag incident" -- the term for acts of vengeance by extremist Jews against Palestinians or Arabs.
The term usually refers to attacks by Jewish settlers on Palestinians or their property in the West Bank, but last year, a similar attack targeted another mosque in another Galilee village.
The desecration of the mosque, which sparked a wave of international condemnation, is believed to be the work of Jewish extremists.
The probe, being conducted by the Shin Bet internal security agency, is largely under a gag order which is in force until October 27, police said.
Earlier, police said they arrested seven more people suspected of joining violent protests in Tuba Zangaria that erupted hours after the arson attack was discovered.
"We arrested another seven people suspected of taking part in the demonstrations, which raises to 25 the total number of people being investigated over the incidents," Rosenfeld told AFP.
Angry Bedouin youths have been demonstrating since the attack, throwing stones at police and torching public buildings, including the local council building, a health clinic and a cultural centre.
Home Front Minister Matan Vilnai said the government would be responsible for fixing the mosque, and helping the village.
"We will do whatever it takes to bring life back to normal, and continue the relations between us and our neighbors, members of other religions living in Israel," he said during a tour of Tuba Zangaria.
Tuba Zangaria lies seven kilometres (four miles) from the northern town of Safed where a local rabbi last year sparked outrage after calling on Jews to avoid renting or selling property to Arabs. (*)
Editor: Kunto Wibisono
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