The Al Jazeera Mubasher Misr office fire in Tahrir Square was carried out by a mob that had been chanting slogans against the Qatari-owned station, according to a studio employee.
The first-floor office used by the station, set up after the uprising that toppled President Hosni Mubarak, was badly damaged by fire.
The studio's windows were smashed and two empty bottles, which had apparently been converted into Molotov cocktails, were found inside the office.
The Interior Ministry described the perpetrators as "trouble makers" who had attacked police officers when they had arrived to investigate, the state news agency reported. The public prosecutor has ordered an investigation.
"There were 200 to 250 people gathered outside the studio chanting against the channel," Ahmed Dessouki, a producer with the channel, told Reuters television.
Civil Protection Forces quickly controlled the fire, and no casualties have been reported.
Witnesses told the state-run news agency MENA that unidentified people were throwing stones at the studio’s office, located on the first floor of a building overlooking Tahrir. Al Jazeera Mubasher Misr itself said earlier that unidentified people threw Molotov cocktails at the building.
Civil Protection Forces are still conducting operations to ensure that fire does not flare up again.
Protesters threw stones and Molotov cocktails at Interior Ministry officials when they went to the square to follow up on the fire. Assistant Interior Minister for Cairo Security Osama al-Sagheer and head of Central Security Forces in Helwan Shoeib Abdu Ibrahim, as well as a number of officers, were among those pelted with the projectiles Wednesday afternoon in Tahrir Square.
Ibrahim was injured and taken to the police hospital in Nasr City.
A Cairo Security Directorate source said that the security manager rushed to the scene accompanied by a fire truck after receiving reports about the blaze.
According to the security source, nearly 500 demonstrators in the square and the surrounding streets tried to take control of the fire truck and prevent it from putting out the flames.
Clashes then started between firemen and demonstrators, the source said. Major General Shuaib Abdu Ibrahim reportedly tried to intervene but was pelted with stones and had to be taken to the hospital.