Police say they dealt with disorder in the vicinity of the Albertbridge Road, Castlereagh Street, Beersbridge Road and Mountpottinger Street areas on Thursday night.
They have come under attack from missiles and petrol bombs thrown from a crowd of approximately 100 people.
One officer was taken to hospital and has since been discharged.
Two people have been arrested in connection with the disorder.
Earlier police moved in to keep a distance between a crowd of nationalists who had gathered in the Short Strand area and a crowd of loyalists.
During the trouble, a car was set alight in the Templemore Avenue area and a burning barricade forced the closure of Castlereagh Street.
UTV's Marc Mallett, who was at the scene, tweeted: "Protesters have blocked Castlereagh Street with burning debris. Large crowd gathered. Heavy police presence".
A PSNI spokeswoman said: "Motorists are advised to avoid these areas". Diversions were in place.
It came after around 100 flag protesters blocked the Albertbridge Road at the junction with Templemore Avenue.
Meanwhile Malton Drive on the Upper Malone Road was closed for a time during a protest, with diversions in place at House of Sport roundabout and Finaghy Road South. The road has now re-opened.
On Wednesday night up to 300 loyalists blocked roads in Carrickfergus.
The demonstration ended peacefully after about an hour.
Last month, Belfast councillors voted to limit the number of days the Union Flag is flown over City Hall.