Disorder sparked in December following a Belfast City Council decision to limit the number of days when the Union flag is flown from official buildings.
Since then, roads have been blocked by loyalist demonstrators calling for the flag to be reinstated. Violence has erupted after some of the protests, with cars and vans hijacked and set alight, and PSNI attacked with petrol bombs and other missiles.
More than 100 police officers have been injured since the flag protests began, and the bill for the policing operation has cost £15.6m.
The PSNI maintain there will be consequences for those taking part in the disorder and the demonstrations, as they probe hours of CCTV footage and other evidence as part of Operation Dulcet.
Superintendent Sean Wright told UTV members of the public are supporting their work but some are still being harboured by their family and friends.
"People are sick of this. They want it to stop. We've had people calling from loyalist communities, identifying those people that we put out in the images and I would ask them to continue to do that."
The team has identified almost 200 new suspects, and dozens have already been brought before the courts.
I think the heftier sentences that we can deliver, the bigger the deterrent factor there will be.
Detective Superintendent Wright
Last month it was revealed that Metropolitan Police, who were involved in the investigation into the London 2011 riots, have been drafted in to assist the PSNI.
DS Wright said his team are investigating a series of offences, including unlawful processions on a Saturday, rioting, vehicle hijacking, and attacks on politicians.
"Every single piece of evidence gathering and CCTV police witness statements that we have collected from the 3rd December all comes into this team," he explained.
Much of the violence has been centred on east Belfast, where police previously claimed senior UVF members were involved in the disorder. Officers have come under attack in Carrickfergus and Newtownabbey, where Mr Wright said the involvement of the UDA is one of his major lines of inquiry.
"Members of those organisations have taken part in the disorder. It would not be our understanding that it has been sanctioned by organisations as a whole," he explained.
But while police have come under criticism for their performance during the protests and not putting a stop to the demonstrations at Belfast City Hall each Saturday, he said people should be assured that they are working behind the scenes.
I would not want the public to think that because we are not stopping the parade on a Saturday that there’s nothing happening about it.
Detective Superintendent Wright
"Those people who are taking part in unnotified unlawful processions, who are rioting, hijacking, attacking people or their premises in the streets, they will feel the consequences of their actions," he explained, adding that an extensive team are gathering evidence to move forward with prosecutions.
"I don't want to be rushing into an ill-prepared case and then that be lost when it gets to the doors of the court. That would be more damaging to the public confidence."
Detective Superintendent Wright also called for those who have taken part in processions or violence to come forward, before police approach them.
"I would encourage them to do that. It would be better you and for your communities that you come to us."