TRANSLINK'S decision to continue to fly the Union flag on designated days has been criticised as 'political'.
The public transport company confirmed that it was responsible for the flag hoisted at its Duncrue Street building, not loyalists protesters as was first thought.
A spokeswoman said it was "a historical thing".
"Duncrue Street is one of our head office buildings, where we have traditionally flown the Union flag on designated days, for example the queen's birthday."
Queen Elizabeth's birthday was on Wednesday.
Translink was unable to say last night how many of its buildings fly the Union flag.
Assembly member John Dallat, a member of Stormont's regional development committee, which scrutinises the body, said it was "unacceptable" for Translink to fly the flag in 2013.
"They should take themselves completely out of the political arena and function as they are intended to," he said.
"There is no need to go to the expense of flag poles and putting up flags which have nothing to do with the services they are supposed to be delivering."
Northern Ireland Water, another body at arms length of government which also receives public funding, has an official policy of not flying the flag.
"NI Water premises are not a government building for the purposes of the Flags Regulations (NI) 2000," a spokesman said.
"NI Water policy is that no flags should be flown from any NI Water buildings at any time."
Translink's own dignity at work policy regards "displays of emblems" as harassment where it has "the purpose or effect of... creating an intimidating, hostile, degrading, humiliating or offensive environment for an employee".
In 2007 a Catholic bus driver was awarded almost £80,000 compensation for religious discrimination after a five-year campaign of harassment which included having a British flag waved in his face.
The tribunal criticised shortcomings in Ulsterbus's investigation into the case, including a lack of official understanding for his concerns.