Five baton rounds were fired and water cannons were used as the PSNI dealt with rioting in the two Co Antrim towns.
A large number of protests took place throughout Northern Ireland on Friday evening, most of them remaining peaceful but causing major road disruption across the region.
Some of the worst trouble was in the West Street area of Carrick.
Police came under attack by crowds throwing petrol bombs, masonry and other missiles.
One of the injured officers required hospital treatment.
Loyalist protestors also threw petrol bombs, fireworks and other missiles in Newtownabbey, where a double-decker bus was set on fire earlier.
All Metro services were suspended in Belfast for the evening after the vehicle was burned out in the O'Neill Road area near the Rathcoole estate. It is understood it was hijacked earlier in the Doagh Road area.
The O'Neill Road roundabout at Cloughfern was closed during the disorder - however police have now confirmed all roads have been reopened.
Two people have been arrested following the trouble.
Thirty-three petrol bombs were thrown in total.
Police will continue to pursue a vigorous evidence gathering operation to bring those involved in the violence to justice.
The trouble flared after protestors threatened to bring Northern Ireland to a standstill, during a series of planned demonstrations across the region.
The rallies dubbed by organisers as 'Operation Standstill' formed part of a continuing loyalist campaign against the decision to restrict the flying of the Union Flag from Belfast City Hall.
Roads were blocked throughout Co Antrim and Co Down, including in Bangor, Newtownards, Castlereagh, Clough, Clonduff, Dundonald, Finaghy, and all across Belfast.
These areas have since been reopened to traffic.
Earlier police said access to Ravenhill Grounds where Ulster Rugby hosted Glasgow Warriors in the Heineken Cup was difficult.
Protests have been held in the region since Belfast City Council voted in December to fly the Union Flag at official buildings only on 18 designated days.
Violence has broken out at some of the demonstrations, with much of the unrest previously concentrating on east Belfast where there were six consecutive nights of violence this month.
Since December, police said over 100 people have been arrested, and over 80 charged in connection with the disorder. Crowds have thrown petrol bombs, fireworks and other missiles at police, injuring nearly 70 officers.
A further flag protest is planned for Belfast City Hall on Saturday, the latest in a series of weekend demonstrations.
Meanwhile, a second peace rally will be held in the city centre on Sunday afternoon.
Last month around 1,000 people took part in a similar rally as a response to the ongoing flag row.
"Like before no speeches and no politicians just the silent majority making some noise," the organisers said of the event.