Fifteen people, including an 11-year-old, have been arrested after trouble erupted in parts of Belfast, Lisburn, Carrickfergus, Armagh and Portadown on Monday night.
A PSNI officer was injured during unrest at Sandy Row in south Belfast where missiles were thrown. A car was also set on fire.
Police came under attack from a group of up to 200 loyalist protesters in east Belfast as they dealt with disorder on the Lower Newtownards Road. There were also reports that a journalist was attacked in the area.
Both areas have now reopened to traffic after crowds dispersed amid a heavy police presence.
Meanwhile UTV understands a police officer was hurt in Portadown after a bottle was thrown in the Shamrock Park area of the town.
Earlier a man was taken to hospital after he was knocked down by a car on the Northway during a flag protest.
In Carrickfergus, police are investigating after a number of protesters stormed the town hall where a public meeting was disrupted and a number of public representatives threatened.
Local Alliance Councillor Noel Williams said about five protesters banged on desks and chairs in what he described as an "attack on democracy."
Police said a crowd of up to 150 people made their way to the public building on Monday evening.
They dispersed the crowd outside before advising those inside when it was safe to leave. No-one was injured.
A 30-year-old man was arrested in the Minorca Place area of the town on public order offences.
Christmas is less than one week away and now is the time to bring this to an end.
ACC Dave Jones
Police also dealt with disorder in the cities of Lisburn and Armagh.
Nine youths have been arrested in Lisburn after what police describe as "serious disorder".
Five boys, the youngest aged 11, were detained in the Hillsborough Road area, while four youths and a 31-year-old were arrested in the Longstone Street area.
A 19-year-old man has been arrested after a firework was thrown at police in Armagh during a protest attended by about 150 people.
Police said around 80 protests took place across Northern Ireland during rush hour traffic on Monday evening as the row over the restriction of the flying of the Union Flag at Belfast City Hall entered its third week.
PSNI Assistant Chief Constable Dave Jones said: "While most of the protests were peaceful, the violence witnessed in some areas tonight is totally unacceptable.
"This is now the third week of protests and I am appealing to everyone involved to take a step back from this. It cannot and should not continue. There were arrests this evening and more will follow as we now trawl through evidence gathered by officers out on the ground.
"I am appealing to those wishing to protest to consider how their actions are affecting the wider community who simply want to enjoy the festive period with their friends and families in peace."
Officers monitored a gathering outside the Alliance Party offices on the Upper Newtownards Road in east Belfast.
The Shore Road was closed for a time at the junction of Mount Vernon Road.
A 25-year-old man was arrested in the Bruce Street area of Belfast on public order offences, while an 18-year-old man was held in the Blyth Street area of the city.
The Crumlin Road at Hesketh Park was also affected by demonstrations - as was Station Road in Whiteabbey.
In Londonderry, the Glendermott Road into the city was blocked at Rossdowney Road.
Coleraine town, Broughshane village and Ballyclare town centre at Rashee Road were also affected.
Police in Ballymena have arrested a 20-year-old for public order offences in the Crebilly Road area.
First Minister Peter Robinson and deputy First Minister Martin McGuinness are expected to hold talks with party leaders at Stormont later this week.
They met with Northern Ireland Secretary Theresa Villiers on Monday to discuss the flags row, which started earlier this month after Belfast Councillors voted to only fly the Union Flag on designated days.
"I have today urged Northern Ireland's political leaders to come together to find a way forward to resolve the ongoing protests on flags," Ms Villiers said.
"It is vital that all the parties work together to make progress towards a cohesive and shared society where decisions on issues like flags can be made in a way which respects different views and takes into account the different traditions and identities of modern Northern Ireland."
On Monday night, UUP leader Mike Nesbitt said: "The Ulster Unionist Party distances itself entirely from all violence. It is time to move on to something more strategic."