A crowd swelled to several thousand with protesters throwing bottles, bricks and fireworks and damaging cars belonging to elected officials. Five police officers, two of them women, two municipal security guards and a news photographer were injured, the Belfast Telegraph reported.
In East Belfast, rioters damaged a Roman Catholic church.
The British flag has flown over City Hall every day for more than a century, since the building opened in 1906. Under the policy approved Monday 29-21 by the City Council, it will fly on 17 days every year.
The Northern Ireland government has a similar policy for its buildings.
Gerry Kelly, a member of the republican Sinn Fein Party who sits on the policing board, called police handling of the protest "disgraceful."
"If that had been 1,000 or more republicans out there, they would not have left it that they were able to come into the back of City Hall," he said.
Christopher Stalford, a City Council member representing the Democratic Unionist Party, criticized the protesters.
"The violence has distracted from the issue we should be focusing on -- the parties in Belfast City Council who have voted as a block to strip the City Hall of its flag."