The building in Carrickfergus, Co Antrim, was attacked and police pelted with stones and missiles after a crowd of up to 1,600 protested against a decision to restrict the flying of the Union flag at Belfast City Hall.
A number of police officers were also hurt in the trouble in the West Street area of the town.
The party offices were targeted because members of the Alliance Party on Belfast City Council voted in favour of the flag being flown only on designated days.
Offices in east Belfast belonging to the party's only MP, Naomi Long, have been picketed and one councillor was advised not to return to her home because of fears for her life. An office belonging to a charity for the disabled was also believed to have been damaged in the fire.
Stewart Dickson, an Alliance Party member at the Northern Ireland Assembly who used the offices, said tonight the building had previous been sprayed with graffiti by loyalists.
He accused the two main unionist parties of whipping up tensions. He added: "This is an outright attack on democracy and cannot be allowed to continue. This campaign of intimidation against the Alliance Party cannot be allowed to continue."
There was serious street disorder in Belfast on Monday night after the city council voted to limit the flying of the flag. Loyalists rioted and at one stage attempted to smash their way into the City Hall.
The east Antrim Democratic Unionist MP Sammy Wilson said there was no justification for the violence in Carrick. Mr Wilson, also the economy minister in the Northern Ireland executive, added: "Those involved do a disservice to the flag they claim to defend. "Today in the House of Commons several MPs backed the Union flag being flown from City Hall. However this criminal behaviour undermines and distracts from the argument."
Police later said they made four arrests in Carrickfergus.