Politically charged fighting between Sunni and Shia Muslims has killed about a dozen people in the ancient city on the fringes of the Sahara desert in the past two months.
Sunni fighters, enraged that their leader was arrested for instigating earlier violence on Friday tried to burn down a radio station; but additional troops and police deployed in the city prevented them from doing so.
"The whole secretariat was totally destroyed. Only the walls were left standing," said a witness, adding that 25 cars were also burned in the local government compound.
A police officer at the scene said: "We found three people with a gallon of petrol and we arrested them."
The government deployed about 500 additional troops and riot police to guard the central mosque and other key areas of the city earlier on Friday, ahead of Muslim prayers that are sometimes a catalyst for violence.
"The government will deal with anyone caught breaking the peace, and already some arrests were made. Adequate measures were taken to protect people, lives and property," Sokoto State Governor, Attahiru Bafarawa, said in a state-wide broadcast before the arson attack.
The dispute in Sokoto is over
Muslim doctrinal differences
Religious, ethnic and communal conflicts have killed more than 20,000 people in Nigeria since it returned to democracy six years ago. The nation of 140 million people is split roughly evenly between Muslims in the north and Christians in the south.
The Sokoto dispute is ostensibly about doctrinal differences between Shia and Sunnis and access to the central mosque.
But Bafarawa, who belongs to an opposition party, has accused members of Nigeria's ruling People's Democratic Party of instigating the violence for political reasons.
The Sunni governor's stance that Shia should have access to the mosque has made him unpopular with some Sunnis.
The region's religious authority, the sultan of Sokoto, has appealed to Sunni and Shia leaders to help stop the violence.
A letter has been circulating in Sokoto since Monday in which Shia are threatened with attacks unless they leave town or renounce their faith at the central mosque. Worshippers say at least 200 Shia have done so.