Unionists have demanded answers after an Irish tricolour was run up the main flagpole of Parliament Buildings at Stormont
It is understood those responsible accessed the pole on the roof of the landmark building in east Belfast without official permission.
The Irish Republic's national flag flew above the home of Northern Ireland's devolved Assembly for around 10 minutes before it was removed. Another unsanctioned flag was erected on an adjacent pole at the same time the tricolour was raised.
Major renovation work has been taking place on the roof this year so more people have had access than in normal circumstances
Democratic Unionist MLA Peter Weir condemned what he branded a "provocative" act and called for an Assembly investigation.
"Whatever the motivation behind this there must be a full explanation from the Assembly as to who had access to the flag poles and who was responsible for this action," he said.
"I have been assured by the Assembly that these were rogue actions and are being fully investigated."
Ulster Unionist MP and MLA Tom Elliott said: "It was no doubt done to attract attention and cause offence and annoyance. The Ulster Unionist Party will be seeking a full explanation of how this could happen.
"We are perfectly clear that the Union Flag is the only flag that should fly over Stormont in order to reflect and respect the sovereignty of the United Kingdom."
The Progressive Unionist Party has said the matter should be probed by the police.
But Sinn Fein accused unionists of over-reacting.
Sinn Fein's Daithi McKay tweeted: "Reaction of unionist politicians to Irish flag over Stormont a bit of a storm in a teacup. Need a flag policy that is inclusive not exclusive."
The flying of flags on official buildings in Northern Ireland is a sensitive issue.
In December 2012, a decision by Belfast City Council to limit the flying of the Union Flag over City Hall triggered months of loyalist protests, some of which descended into violence.
Like the policy adopted at City Hall, the Union flag is only flown on Parliament Buildings on a number of designated days each year.
But politicians have to date failed to agree a comprehensive framework for managing the flying of flags on public buildings and on lamp posts in republican and loyalist communities across Northern Ireland.
The Police Service of Northern Ireland (PSNI) said it was aware of the incident and was investigating the circumstances.
An Assembly spokeswoman said: "The Northern Ireland Assembly was made aware that two flags were flown without permission from the roof of Parliament Buildings for a short time today.
"The roof and the fourth floor of Parliament Buildings are currently a construction site under the control of building contractors.
"As soon as the Assembly was made aware of the incident, the flags were removed. The Assembly is investigating the incident."
Assembly officials are due to brief elected members who sit on the Assembly Commission body on the incident tomorrow.
Sinn Fein MLA Gerry Kelly said there was a need for respect for all traditions at Stormont. He said unionists seemed more interested in the flags incident than the current budgetary crisis facing powersharing.
"The reaction by unionist politicians to the hoisting of two Irish flags above Stormont's Parliament Buildings can only be described as hysteria," he said.
"This for some unionist politicians is a bigger crisis than anything that has happened over the past weeks.
"One thing that is lost on those who are objecting is the fact that they are the same parties who have not called for the removal of countless British and unionist flags at sensitive interfaces or from countless town centres bedecked with Union Flags.
"Stormont has only just finished a consultation into flags and emblems in the grounds of Stormont and parliament buildings and one thing will be very clear; there is nothing about the place that celebrates or respects the nationalist tradition in this part of the island.
"We want to create an environment based on respect and tolerance and we would call on those who are now objecting so strongly to this incident to join with us in creating a policy that reflects that."