The total cost to date was revealed by Assistant Chief Constable Will Kerr during a meeting of the Policing Board on Thursday afternoon.
It covers the three months of loyalist demonstrations which have taken place since December, when councillors in Belfast reduced the number of days the Union flag flies at City Hall.
It was also highlighted that 213 people have now been arrested - 80% of whom were previously known to police.
The Policing Board meeting came after unionist politicians - including DUP leader Peter Robinson - publically raised concerns over a "perceived unfairness" in the policing of flag protests.
I will not be silenced when I see the need to speak.
First Minister Peter Robinson
Responding to suggestions that he should not have commented, Mr Robinson said: "I want to make it absolutely clear that I re-affirm and stand by the contention that there are genuine perceptions within Unionism about inequalities that need to be addressed."
In his statement titled 'I will not be silenced', the First Minister added: "Neither the Chief Constable nor the Lord Chief Justice can be immune from the need for these perceptions to be addressed.
"They have a responsibility to deal with these matters and to explain the facts and circumstances. Such explanations are necessary and indeed beneficial to strengthen the operation of the criminal justice system."
However, an SDLP member of the Policing Board has called on Mr Robinson to apologise in the wake of the new figures, which he said show that "the vast majority of those arrested have form".
Conall McDevitt MLA added: "Peter Robinson has been stoking tension and playing fast and loose with the facts for 13 weeks now. It's time for him to accept the simple facts of the matter and apologise for being so irresponsible.
"He is meant to be the First Minister for everyone. The time has come for him to get back to work and stop indulging the anti-agreement elements at the heart of the flag protests, who are just interested in destroying the progress made to date and dragging our society back."
PSNI Chief Constable Baggott has strongly denied the accusations of bias.
On Wednesday, the Lord Chief Justice Sir Declan Morgan also addressed the issue with a statement from his office insisting that judges should be free to act without "improper influence".
I think it's dangerous to start playing with statistics. I am very happy to provide the statistics of arrests and charges over the last year, two years and three years - but they don't tell the story of what was happening at the time.
Chief Constable Matt Baggott
On the subject of the policing costs, Mr Baggott added that it was a "waste" of resources.
"That money should have been spent on tackling drug dealers," he said.
"It should have been spent on officers patrolling in the heart of our most disadvantaged areas; it should have been spent on people trafficking; it should have been spent on new technology.
"It's been wasted dealing with disturbances and disorder that should never have happened in the first place."
While the street protests have continued into March, the violence which followed some of the earlier demonstrations appears to have calmed.
Officers from the PSNI's Operation Dulcet inquiry team are continuing to investigate offences linked to the flags dispute.
Meanwhile, the Backin' Belfast campaign has been set up to alleviate the financial losses to the city incurred at the height of the unrest.