Assistant Chief Constable Alistair Finlay met with community representatives and politicians in Newtownabbey on Sunday, amid criticism that the PSNI had not consulted with local residents before taking down "a limited number of flags" in the Grange Drive and Doagh Road areas of the town.
"I offered my sincere apologies to those people who felt that they have not received the Police Service that we strive to deliver," said ACC Finlay after the meeting.
"That said nothing excuses the violence that was experienced last night. The people involved in carrying out these attacks are causing hurt and fear in their own communities.
Up to 100 people gathered in the town at around 11.30pm on Saturday, throwing petrol bombs and missiles at police. Trouble also erupted in Newtownabbey and Carrickfergus.
Police say 15 vehicles were hijacked, including two buses. A number of these were set alight and used to attack police lines.
Five officers were hurt when a police vehicle was rammed with a hijacked bus in Ballyclare. Another officer was injured when he was hit with stones.
Police fired baton rounds and used a water cannon in the town before calm was restored at around 2.30am on Sunday.
Residents claim the flags which were taken down were not illegal and commemorated those who fought in the Battle of the Somme.
ACC Finlay said a review will be conducted into "how we reached our decisions and the actions that we took so that we can learn for the future."
At a press conference on Sunday, local area commander Derek McCamley defended his decision to remove the flags outside a Catholic church, in compliance with joint protocol.
"Each case must be judged on its own merit and my officers have worked and will continue to work tirelessly with all the interested parties - local representatives and the community to try to find solutions that accommodate everyone.
I understand that flying flags is a popular way of displaying tradition and culture in Northern Ireland. But for others it is an emotive issue.
PSNI Area Commander Derek McCamley
"We would urge local people to work with us towards a resolution that is sensitive to the interests and feelings of everyone in the community."
Mr McCamley said the violence was led by a group of young people.
"It is too early to say yet if paramilitaries are behind the disturbances, but a number of youths were involved."
"The Police Service takes a very robust approach to anyone engaging in criminal activity or putting the community at risk. An ongoing investigation into last night's disturbances is underway."
PUP representative Phil Hamilton denied any illegal organisations were involved in the trouble.
"I don't think there's paramilitaries involved in it. I think we've seen a community at boiling point and it just shows what can happen, people's tempers and patience have just gone thin.
"What I do think this has been is the community venting its anger against the PSNI and their reckless decision to remove the Union flag."
Mr McCamley refuted the local communities had called for his resignation.
"I've not been Area Commander for Newtownabbey and Carrickfergus for that long, but I would not say any decisions I've taken have been rash," he added.
Justice Minister David Ford said police officers acted entirely in accordance with protocol.
"They bear no blame for what happened on Saturday night: the blame lies entirely with those who fomented the riot and those who caused fear and mayhem in Ballyclare," the South Antrim Alliance MLA said.
However DUP MLA for the area Paul Girvan said he believed the PSNI had "overreacted".
"On Saturday, police were on the street and a number of paramilitaries arrived to put up flags and replace the ones that were put down. I think they put up tenfold what was removed, as a statement.
"There was a heavy police presence on Saturday night and as a result tensions were high because police didn't only remove paramilitary flags, they also removed Union Jacks and Ulster flags, which sent out a message to the wider community that they felt very much under threat."
East Antrim DUP MP Sammy Wilson said the riots were a worrying development for everyone in Northern Ireland.
"This shows there is a degree of orchestration, it's not just spontaneous and it's coming at a time when we should be celebrating. Instead we're getting all these negative images all around the world.
"In most places it's been agreed the flags will go up and come down again after the Twelfth.
"The police have to be sensitive about how they handle this flags issue, although that's no excuse for what has happened."