Twenty-six people were arrested during rioting in nationalist areas of north and south Belfast and Londonderry after Tuesday's Orange Order parades.
Sixteen police were injured and officers fired 55 plastic baton rounds - all of them in north Belfast's Ardoyne area.
Police said children as young as 10 were involved in the rioting in Derry.
Rioters threw petrol bombs, bricks, stones, fireworks and bottles at officers during the trouble.
Twelve arrests were made in Derry, nine in Belfast's Ardoyne - including a 12-year-old boy and five in the Markets area of south Belfast.
In Armagh, there were reports of public disorder in the Friary Road and Killylea Road areas, while in Ballymena a car was burnt out in Dunclug estate.
Assistant Chief Constable Alistair Finlay said those involved in the violence were mindless thugs and there was no evidence that it had been orchestrated.
He said an officer whose helmet was set on fire by a petrol bomb was already back on duty - a testament to his bravery and also the quality of the riot equipment the police use.
The trouble in north Belfast broke out after police in riot gear took up position ahead of an Orange parade walking past Ardoyne shops on Tuesday evening.
A crowd of about 200 people threw petrol bombs and other missiles at police who responded with a water cannon and by firing a number of plastic baton rounds - one of which hit a photographer.
Police said a number of officers were injured.
ACC Finlay said the scale of the violence had been "intense".
"The vast area of Northern Ireland was extremely peaceful, yet for these few streets we get headlines of violence, of people injured, of communities and relationships being broken, and infrastructure and property damaged," he said.
"There will be a follow up operation like last year and people will be brought before the courts."
In 2010, there were several days of rioting after the parade was allowed to walk past the shops.
The Greater Ardoyne Residents Collective (GARC), which opposes the Orange parade passing the nationalist Ardoyne, held a protest in response to the Parades Commission decision to allow the march to pass the shops.
Sinn Fein MLA Gerry Kelly said a parade in the area would continue to be a problem.
"The difficulty was that there was an Orange parade," he said.
"People have made great efforts, but a parade coming through a Catholic area is a problem.
The DUP MP for North Belfast Nigel Dodds said people had to realise that the Crumlin Road was a "shared space and not just a nationalist road".
"The people engaged in the violence didn't even see the parade go past," he said.
The trouble in Derry broke out in the Bogside and Fahan Street areas and in Gobnascale and Ardmore in the Waterside, while there was also violence in nearby Strabane and Castlederg.
Among those arrested was a 14-year-old boy. A crate of petrol bombs was also recovered in the Fahan Street area of the city.
A group of Spanish tourists, who had just left their hotel, narrowly escaped injury when petrol bombers attacked police.
In the Markets area of Belfast, a number of youths threw stones and missiles at police in Stewart Street and a car was set on fire.
On Monday night, 22 police officers were injured during serious rioting in several nationalist areas of west and north Belfast.
On the Twelfth of July, the Protestant Orange Order takes part in demonstrations across Northern Ireland, commemorating King William of Orange's 1690 Battle of the Boyne victory over Catholic King James II.