The Police Service of Northern Ireland (PSNI) assistant chief constable Alistair Finlay had earlier singled out First Minister Peter Robinson and Deputy First Minister Martin McGuinness for criticism after violence surrounding July 12 Orange Order marches left 82 officers injured.
Chief Constable Matt Baggott blamed dissident republicans opposed to the peace process for fomenting tensions that reached a height in the Ardoyne area of north Belfast last night where police came under sustained attack and eventually used baton rounds and water canons to contain rioters.
Mr Baggott declined to single out individual politicians for criticism over the marches issue but called for a "big debate" on the way forward.
Mr Robinson and Mr McGuinness later issued a joint statement condemning the violence and highlighted their efforts to secure a lasting solution to tensions over controversial marches.
DUP leader Mr Robinson said: "I am disgusted at the outright thuggery and vandalism that has taken place over the course of the last 48 hours.
"There is no excuse and no place for violence in civilised society. Both the deputy First Minister and I have been, and will continue, to work for a resolution of the difficulties around parading."
Mr McGuinness said: "Our experience demonstrates that the way to deal with any disputes or contention is through dialogue and agreement.
"There are numerous examples that show this to be the way forward.
"We are currently consulting on legislation that aims to provide a workable framework for dealing with contentious parades."
But the First Minister Mr Robinson added: "I am disappointed to hear some of the comments from ACC Finlay and look forward to meeting with the Chief Constable shortly to discuss the events of the last 48 hours and ACC Finlay's unhelpful and unacceptable remarks.
"We must keep our entire focus on defeating those who would seek through violence and destruction to drag us back."
While 82 officers were injured in riots over the last 48 hours, a total of 55 officers were injured in last night's rioting alone.
On Sunday night three officers suffered pellet wounds during riots in Belfast when they were fired at by a man armed with a shotgun.
Yesterday there were disturbances in a number of areas including parts of Belfast, in Lurgan in Co Armagh, and in Londonderry where a masked man armed with a handgun shot at a police vehicle, though officers escaped injury.
In Lurgan rioters stopped the Belfast to Dublin train and tried to set fire to it. The driver managed to restart the train and leave the scene before any of the 55 passengers on board were injured.
Meanwhile, the Chief Constable today released dramatic footage captured from a police helicopter that showed how officers came under frenzied attack from rioters in Ardoyne.
It showed a line of riot police being repeatedly attacked by masked men armed with iron bars and wooden posts. Mobs were also shown launching sustained attacks on armoured police vehicles.
While police eventually fired baton rounds, Mr Baggott said the police images showed that his officers had displayed great restraint.
In the most serious incident of the night a female police officer had a concrete block hurled on to her head. She remains in hospital where she is said to be stable.
Mr Baggott said that while exact figures were not yet available, the violence would cost millions of pounds.
He implicated dissident republicans in the riots, which he said included teenagers and children as young as eight.
The police chief branded the disturbances as a dangerous cocktail of "recreational rioting with a sinister edge".
Mr Baggott said: "The cost of policing last night in that small part of Northern Ireland is the equivalent of a ward in a hospital, it's the equivalent of a primary school, it's the equivalent of neighbourhood policing.
"And it is time to have that big debate about what is really important for the future in Northern Ireland."
Earlier ACC Finlay singled out Mr Robinson and Mr McGuinness for criticism and said they had been silent prior to July 12 and in the immediate aftermath of the Ardoyne violence.
"We didn't see joined-up, strategic leadership," he said.
Mr Baggott did not go as far as his colleague, but called for society to speak out with one voice against violence.
The vast majority of parades pass off peacefully on July 12, the height of the loyal orders' marching season.
But in a relatively small number of locations parades continue to cause tensions between rival communities.
DUP leader Mr Robinson and Sinn Fein's Mr McGuinness were central to negotiations at Hillsborough castle earlier this year that brokered deals on the devolution of policing powers and on creating new legislation on parades.
Last week the Orange Order rejected the draft proposals which would replace the government-appointed Parades Commission, with a new system to broker local solutions to parade stand-offs.
Leader of the nationalist SDLP Margaret Ritchie said rioters had caused "a massive trail of destruction", but she blamed the DUP/SF parade proposals for adding to instability.
A residents group at the centre of a controversial protest against the march at Ardoyne today tried to blame the Orange Order for the resulting disturbances.
In a statement the Greater Ardoyne Residents Collective said: "Firstly, our analysis proved correct, Loyal Orders who insist on coat-trailing acts of bigotry through our area, permitted by the detached Parades Commission and last but not least, the PSNI who once again are seen in the eyes of the world, ready and willing by any means necessary to ensure the greater Ardoyne community is subject to intimidation and humiliation."
In an apparent swipe at Sinn Fein, the group added: "So much for the Ireland of Equals, where do we fit in?"
But Sinn Fein's Gerry Kelly said elements with no support in areas such as Ardoyne were fomenting tensions. He blamed dissident republicans for the violence and said petty criminals had also used the July 12 tensions to become involved in rioting.
Acting chairman of the Policing Board Brian Rea condemned the disturbances: "It is clear that despite the best efforts of community and political representatives, a small minority were intent on causing maximum disruption and inflicting terror on police and the wider community."
Northern Ireland Secretary Owen Paterson praised the police and condemned those behind the violence as "cynical enemies of the whole community".
"Northern Ireland has come so far because locally elected, locally accountable representatives have found the political will to resolve difficulties that not so long ago seemed insoluble," he said.
"I have no doubt that will be the case with parades.
"But there will be those who will try to exploit and create community tensions.
"They will not be allowed to put the future at risk."
