Two hundred and sixty people have already been convicted.
The officer in charge of Operation Titan, Det Supt Sean Wright, appealed for anyone taking part in planned protests later this month to do so lawfully and peacefully.
Operation Titan was set-up to investigate public order-related incidents since 12 July.
Police released the figures at a press conference at PSNI headquarters in Belfast on Monday.
ACC Will Kerr said 2013 had been a challenging year for policing.
He said the last four years had seen a severe dissident republican threat, however recently there had been an upsurge in activity.
In relation to the loyalist paramilitary group, the UVF, ACC Kerr said that elements of the group, particularly in east Belfast, had been involved in a range of criminal activity, however the issue of respecification was a political decision.
Police have said 560 people have been charged or reported in connection with flag protests in Northern Ireland.