The secretary of state has urged Northern Ireland politicians to move quickly to take responsibility for parading issues.
Twenty police officers were injured and up to 10 shots fired at police after trouble flared overnight in Ardoyne, north Belfast.
It followed two parades along a stretch of road dividing Catholic and Protestant communities.
Owen Paterson said he thinks things should be done differently.
"The parades commission was lawfully constituted by Parliament in 1998 in order to take decisions over parades out of the hands of the police and politicians," he said.
"Should local politicians agree to alternative arrangements, and take responsibility for parading as was envisaged in the 2010 Hillsborough Castle agreement, the government will support them.
"In the meantime we shall stand by the independent parades commission as the sole legal authority in Northern Ireland to make determinations on parading."
The first parade was by a small group of Orangemen returning from the annual Twelfth of July celebrations.
The second was by a nationalist group opposed to the parade.
Petrol bombs and bricks were thrown at police lines by both nationalists and loyalists.
After midnight shots were also fired from the nationalist side but no police officers were hit.
Police fired six plastic bullets and used water cannon on the crowds. None of the injuries caused to police officers were serious.
Four men aged between 18 and 41 have been charged with public order offences.
PSNI Chief Constable Matt Baggott said those involved had no reason to attack the police.
"There is no excuse for rioting and violence, albeit it was contained in a relatively small area of Northern Ireland," he said.
"We will be bringing many people to court in the days that follow.
"In time, we will have to understand more about why some parts of Northern Ireland are falling behind and that's a challenge for us all, politicians, police and community alike."
Assistant Chief Constable Will Kerr said the community needed to call a halt to the violence.
"I am angry that we have these three days of annual madness where it seems that everybody thinks the peacekeepers are a legitimate target," he said.
"We will be making a significant number of arrests, as we did last year, over the course of the next weeks and months to make sure that people are placed before the courts and answer for their decisions."
DUP MP for North Belfast Nigel Dodds condemned the decision by the Parades Commission to allow a nationalist protest parade to take place in north Belfast.
"I blame entirely the Parades Commission who permitted this parade by a dissident republican crowd intent on trouble," he said.
The Parades Commission is an independent, decision-making body set up to make decisions about contentious parades in Northern Ireland. It can place restrictions on marches, but it does not have the power to ban them outright.
Its chairman Peter Osborne said it was nonsense to blame the overnight violence on the commission.
He said they had been facilitating mediation in north Belfast for more than 11 years.
"Of the 4,000 parades across Northern Ireland, almost all of them go without restrictions.
"We have to balance the rights of everybody concerned in parades, not just the rights of paraders, but the rights of people who live in the areas and the rights of police officers."
Mr Osborne said that the judgement made was the best in the circumstances.
"The question you have to ask others is: 'What would they do?' It is time local politicians took ownership and responsibility for the parading issue. Until they step forward and take decisions, it will be left to the Parades Commission. It is almost impossible when people stand on sidelines and criticise."
During the violence in north Belfast, three cars were hijacked and two of them pushed at police. At least one of them had been set alight.
There was "significant disorder" in the nationalist Brompton Park and Balholm Road areas. A short distance away police were attacked with bricks and bottles thrown by loyalists on the Crumlin Road near the junction with Hesketh Road.
On the other side of the Ardoyne flashpoint at Twaddell Avenue, bricks and bottles were also thrown at police by loyalists.
Some nationalists object to the parade which marks William III's victory at the Battle of the Boyne in 1690.
Earlier, 24 Orange Order marchers completed a token parade in the area.
The trouble broke out after Protestant Orangemen, who are members of north Belfast lodges, walked along a section of the road which runs alongside Catholic homes and shops.
A protest by Catholic residents to show their opposition to the Orangemen walking past the area was held along with a parade by the group Greater Ardoyne Residents Coalition (GARC).
"The Greater Ardoyne Residents Coalition parade was delayed at Estoril Park by agreement due to a public safety issue caused by the significant disorder and a burning vehicle," said Assistant Chief Constable Kerr
"Once this was cleared, the GARC parade continued on to the Crumlin Road.
"Missiles were thrown from both sides as the GARC parade passed the Ardoyne shop fronts but both the parade and the protest dispersed.
"Police would like to take this opportunity to acknowledge the positive efforts of all those parading, protesting and marshalling on Thursday."
Earlier, police said the Orange Order parade had passed "peacefully" and "in accordance with the Parades Commission determination".
The representatives of three Orange lodges, carrying three banners, were escorted by riot police as they walked past Ardoyne.
The marchers were completing a controversial parade within a deadline set by the Parades Commission.
There was some shouting from nationalist protesters as the small group of marchers went past.
Hundreds of loyalists were waiting to welcome them when they had passed the contentious area.
The marchers had been taken to north Belfast by bus to meet the 16:00 BST deadline.
Orangemen said it was a peaceful solution to allow them to complete their return parade from the main celebrations to their Orange halls in north Belfast.
Following Thursday night's violence, Sinn Fein MLA for North Belfast Gerry Kelly said: "If the Orange marchers did not march through these areas, then the trouble would not happen.
"The Orange parades went out in the morning, they were able to celebrate their culture, meet old friends etc, no-one is against all of that. But why would they insist on coming back afterwards to that area which is contentious?"
Councillor Brian Kingston was one of the Orangemen who paraded past the Ardoyne Shops.
"The aim here is to create a more normal society. A small number should be able to come down and return home. It is right they should be able to return home," he said.
In a statement, GARC (Greater Ardoyne Residents Collective) said: "We only wish the media and unionist politicians, including the first minister, were as concerned about the inconveniences that the residents of our areas face as a result of unwanted loyal order parades."
There was some trouble in Craigavon after a bus was hijacked in the Drumbeg estate.
In Londonderry, petrol bombs were thrown in the Westland Street area and at the city's walls. Cars were set alight in Fahan Street.
Meanwhile, six men aged between 18 and 34 have been charged in connection with rioting in the Broadway area of west Belfast on Wednesday evening.