The suspects were allegedly found with explosive materials, Israeli radio reported.
Israeli Arabs clashed with police Monday after the fire was discovered, officials said.
A march by 300 residents from Tuba to nearby Rosh Pina turned violent when marchers started throwing stones and setting fire to tires, The Jerusalem Post reported. Police, who pushed demonstrators back into the village with tear gas and stun grenades, worked to calm tensions, Haaretz said.
The fire caused severe damage to the mosque's carpet and inner walls, a police spokesman said. Graffiti sprayed in the area said "revenge" and "price tag."
A special task force was created last month to crack down on so-called "price tag" incidents in the West Bank. Two West Bank mosques have been vandalized with the same graffiti.
Defense Minister Ehud Barak condemned the arson attack, calling it a "criminal act that harms the state of Israel."
Barak said the mosque attacks "are destabilizing relations between Jews and Arabs and are causing great harm to the name of Israel in the world."
Public Security Minister Yitzhak Aharonovitch called the mosque fire a "criminal and despicable attack on a holy place," The Jerusalem Post reported.