Mr Baggott launched a scathing attack on the Orange Order on Saturday, branding their call for protests on the streets, which descended into violence, as reckless.
Trouble broke out on the Twelfth after the PSNI prevented an Orange Order march from passing the Ardoyne shop fronts, in accordance with a Parades Commission ruling.
Twenty officers were injured as missiles including bottles and bricks were thrown during six hours of rioting.
North Belfast DUP MP Nigel Dodds, who is also a member of the Orange Order, was hit on the head by an object thrown by loyalists at police and had to be taken to hospital by ambulance.
Over 30 baton rounds were fired causing a number of injuries.
There was also disorder in the lower Newtownards Road area of east Belfast. Twelve police were injured and one suffered a suspected broken jaw.
A mutual aid officer - one of 630 drafted in from England, Scotland and Wales to assist the PSNI - had her leg broken. Six officers in total had to be taken to hospital.
Four hundred extra police officers from Great Britain have been deployed to Northern Ireland following Friday's troubles.
The Orange Order had called for demonstrations ahead of the Twelfth against the Parades Commission's determination.
Grand Chaplain Mervyn Gibson said that call has now been suspended.
He continued: "In support of the Grand Orange Lodge of Ireland's appeal for calm, the Ligoniel lodges - with the full support of the County Grand Orange Lodge in Belfast - have decided to suspend their protest in relation to the determination for the Crumlin Road."
The scenes were both shameful and disgraceful.
Matt Baggott said some of the leadership from the order had been "reckless" and "compromised the safety of many people".
He continued: "Some of the leadership within the Orange Order need to reflect upon whether they provided the responsible leadership asked for by myself and by the party leaders
"Some of their language was emotive and having called thousands of people to protest they had no plan and no control and I think the word for that is reckless. Not to have a plan, not to have control compromised the safety of many people."
There were 4,000 police on the streets of Northern Ireland on Friday evening.
Assistant Chief Constable Will Kerr said: "We had officers who were knocked unconscious, officers with head, leg, other limb and eye injuries.
"Two of the officers injured were mutual aid officers. The female officer with a suspected fractured leg was in very good spirits this morning."
Seven people were arrested in south and east Belfast for a range of offences including common assault and disorderly behaviour.
Missiles were thrown as the Twelfth parade made its way onto the Lower Newtownards Road, some towards houses in the Short Strand from the Strandwalk direction.
A PSNI spokesman said eight police were injured protecting St Matthew's chapel.
Police were also attacked by nationalist crowds in the Short Strand.
In a statement they said: "Within the Short Strand officers were attacked with missiles, thrown by individuals from within this community. Police officers deployed water cannon to manage public disorder in the lower Newtownards Road area."
Chair of the Policing Board, Anne Connolly, condemned the violence.
"The number of officers injured while doing their job is shocking and completely unacceptable," she said.
"It is important that those involved in disorder and violence understand that there are consequences to their actions and that they are charged and prosecuted. I would like to wish the officers and others who have been injured as a result of this violence a full recovery."
Secretary of State Theresa Villiers said: "This sort of behaviour does nothing to promote 'Britishness' or the pro-union cause. Rather it undermines it in the eyes of the overwhelming majority of people here in NI and in the rest of the UK.
"Once again I pay tribute to the bravery of the Police Service of Northern Ireland and officers from Great Britain who did such an outstanding job in upholding the rule of law. They deserve our utmost praise and support."
The Chairman of the Police Federation for Northern Ireland, Terry Spence, said: "This whole episode of protest has brought nothing but shame on the protestors and their political and community representatives."
Mr Spence also paid tribute to the officers from England, Scotland and Wales who were brought in to assist the PSNI.
"Without their help last night we may well have been overwhelmed," he said.