Belfast City Hall's union flag has been lowered after flying for the first time since a decision was taken not to display it permanently.
The vote by Belfast city Council on 3 December sparked a campaign of protests, some of them violent.
The flag flew on Wednesday to mark the Duchess of Cambridge's 31st birthday.
Flag protests have taken place in Belfast and Londonderry on Wednesday evening, but there have been no reports of any trouble.
The Northern Ireland secretary of state has said riots linked to the protests are causing "significant damage" to the economy.
Theresa Villiers said the "negative images" were "threatening jobs".
She described the violence as "appalling".
"Those who have been trying to bring Northern Ireland to a standstill need to take a long, hard look at what it is they think they're achieving," she said.
"I can understand that feelings run high when it comes to issues on flags, particularly in Northern Ireland where questions of identity remain so sensitive.
"But nothing can excuse the scenes we have witnessed, with over 60 police officers injured."
Ms Villiers said it was "incomprehensible" to express patriotism and support for the union by "hurling bricks and petrol bombs at police".
"These violent protesters are damaging the cause they claim to support," she said.
The cost of policing the protests is believed to be over £7m.
Some of the protests have been violent and resulted in more than 100 people being arrested and dozens of police officers sustaining injuries.
Loyalists have made it clear they will continue their protests.
Their central demand is for the decision to fly the union only on designated days to be reversed but the political make up of the council means there is little chance of that happening.
Meanwhile, the chairman of the Families Acting for Innocent Relatives group has said a planned loyalist protest in Dublin on Saturday will not take place as scheduled.
Barry Halliday, who was assisting loyalist activist Willie Frazer in organising the protest, told RTE News that it had been "put on hold" following contact with Irish police.