The Real IRA has been blamed by Sinn Fein for trouble in north Belfast.
At least one shot was fired at police by republicans and there were other disturbances after Orange Order parades across Northern Ireland.
Twenty-three police officers were hurt across Northern Ireland and baton rounds and water cannon were used.
In the Ardoyne area of Belfast 21 police officers were injured and three vehicles were hijacked. Rioters also threw two blast bombs.
Police said they fired 18 baton rounds.
A BBC reporter saw a masked rioter fire a single shot from a handgun towards the police.
A loaded rifle was also handed into police after a group of children were seen playing with it.
Ardoyne priest Father Gary Donegan said the trouble was started by outsiders.
"Myself and many people were looking at people last night that we'd never seen in the area before in our lives.
"It was as if people had been bussed into the area for this very purpose and that this was being very much orchestrated," he said.
Violence in the area continued into Monday night, with petrol bombs, fireworks, stones, and bottles thrown at police after they tried to move rioters away from a parade route.
Two of three vans which were hijacked were pushed at police lines.
Police promised a "rigorous investigation" to identify those who had taken part in the trouble.
Incidents also took place in several other towns across Northern Ireland.
In the early hours of Tuesday, police and Army bomb disposal experts were called to a security alert in Lurgan, County Armagh. It was sparked by a suspicious object in a car that was hijacked earlier. It was later declared a hoax.
There was a similar incident in Strabane, County Tyrone.
In the Memorial Hall area of Londonderry, 11 petrol bombs were thrown during Monday's disturbances, but there were no reports of any injuries or arrests.
Earlier rival groups had taunted each other as Orangemen and a small number of bands made their way through the city's Diamond area.
Both sides spat at each other and threw missiles. Police separated factions, but were themselves attacked by nationalists throwing stones and bottles.
NORTHERN IRELAND TROUBLE
In Armagh, police came under attack with missiles and paint following a security alert at Friary Road in which a minor explosion occurred.
Four people have been arrested for public order offences and at least two cars were also stolen and set alight in the city.
In Rasharkin, County Antrim, officers also sustained minor injuries when they were struck by stones and bricks. One man was arrested.
'Bigotry and intolerance'
PSNI Assistant Chief Constable Alistair Finlay said it was disappointing "isolated outbreaks of violence had marred the day for all communities".
He said: "Right across Northern Ireland there were hundreds of parades that passed off peacefully.
"However, it is very disappointing that there were a minority of people, in north Belfast, Derry, Armagh, Rasharkin and other parts of Northern Ireland who showed total disregard for local communities.
"They displayed the worst possible face of Northern Ireland - a face of bigotry, sectarianism and intolerance that is not representative of the vast majority of people."
Sinn Fein's Gerry Kelly said a "a small number of dissident republicans from outside Ardoyne" had stoked sectarian tensions and orchestrated the trouble.
He said: "The Real IRA or whatever they may call themselves and some other splinter organisations sent people over here with the sole aim to cause riots, to bring this further down into sectarianism."
The Sinn Fein leader Gerry Adams condemned the violence and said the Orange Order should consider re-routing a small number of contentious parades, including those which pass the Ardoyne.
"Why play into the hands of those who orchestrated last night disturbances?," he said.
"I would appeal to the Orangemen - they're not giving a victory to anyone if they just take an alternative route to where they want to go."
He also called for the leadership of the Orange Order to talk to Sinn Fein.
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