Several police officers were injured in the early hours of this morning in what was described as "serious public disorder" in Ballyclare Co Antrim.
Petrol bombs and other missiles were thrown at police and a bus was hijacked and used to ram a police vehicle.
The violence flared at about 11.30pm last night when a crowd of up to 100 people began throwing missiles.
A number of baton rounds were fired and water cannon was deployed. Calm was restored to the area by 2.30am.
Disturbances were also reported in Carrickfergus and Newtownabbey.
At about 3am police were called to the Leckagh Drive area of Magherafelt Co Derry to trouble involving up to 50 people close to a bonfire.
Police were attacked by missiles as they tried to remove a barricade.
A number of homes were also targeted in attacks which police described as sectarian.
A 27-year-old man was arrested for riotous behaviour following the disturbances in Magherafelt.
Loyalists in Co Antrim have been protesting after accusing police of removing flags. This is the traditional marching season for the Orange Order and many Protestant districts are flying flags and bunting.
Nationalist SDLP MLA Conall McDevitt said there had been a significant escalation in the flying of paramilitary flags across Northern Ireland this summer.
"This has caused considerable distress in communities on both sides of the divide," he said.
"The police cannot fix the problem of flags long-term, but it must be fixed politically and with real leadership from the top.
"It is with deep regret that for the past five years Sinn Féin and the DUP have failed to progress the establishment of a meaningful flags protocol, which would control the flying of flags, particularly in contentious situations."
The Catholic Bishop of Down and Connor Noel Treanor this afternoon condemned the violence and called for an atmosphere of respect during the marching season.
"Nobody wants these destructive acts, not least of all local residents. They endanger life, hurt us all and damage hope for the future.
"This violence wrecks our tomorrow. It robs our children of future jobs and
opportunities."
He asked those attending parades or protests to avoid committing acts of
provocation.
"I call on all leaders, groups and organisers to ensure that events are not
manipulated by destructive influences from outside the communities where parades take place," he added.
The chairman of the Northern Ireland Policing Board Brian Rea condemned those responsible for last night's disturbances.
"The violence in these areas is worrying and this morning communities have literally been left picking up the pieces. Our police officers have once again come under attack but thankfully injuries are not serious," he said.
"I join with other political and community representatives in calling for calm
and over the next few days. Further disorder is in no ones interest."
Meanwhile, the only march by the Orange Order south of the border passed off without incident yesterday.
The march, in Rossnowlagh Co Donegal, has been taking place since 1978.
Edward Stevenson, grand Master of the Orange lodge in Ireland, said the march enabled them to celebrate their "British culture and identity" in the Republic.
"We are a threat to no-one. In fact the people here want to play their part in the civic society of this country, " he said.
Mr Stevenson paid tribute to the "tremendous and dignified welcome” given by people in the Republic to Queen Elizabeth on her recent visit.
Additional reporting: PA