TUV leader and North Antrim MLA Jim Allister raised the issue of the flag not being flown at Ballymena Courthouse on 6 February, in a written question to Justice Minister David Ford.
Mr Allister wanted to know why the flag wasn't flown, what action had been taken and what steps had been taken to ensure it didn't happen again.
Mr Ford confirmed that security provider G4S was responsible for ensuring the designated days policy was upheld at all court buildings.
"G4S were asked for an immediate report on why this failure occurred and have advised that it was due to human error," the Alliance Party leader added.
"The NICTS Chief Executive is meeting the Northern Ireland Managing Director of G4S urgently to discuss this matter. Any disciplinary action will be a matter for G4S."
We would like to apologise for any offence this oversight may have caused.
In a statement, a G4S spokeswoman told UTV that not flying the flag on the day in question had been due to an "oversight".
"Following an internal investigation, G4S has taken immediate corrective action to ensure compliance with flag flying requirements," she said.
"All staff have been reminded to ensure that correct procedures are followed on designated flag flying days."
The flying of Union flags has been at the centre of ongoing tensions since 3 December, when a motion was passed by Belfast City Council to adopt a designated days policy at Belfast City Hall.
A motion to stop flying the flag completely was tabled by Sinn Féin and the SDLP, but was amended by the Alliance Party to allow the Union flag to be flown on 18 designated days.
Unionist parties voted against any restrictions being put in place.
Flying the flag on designated days brings the policy at City Hall into line with Stormont and other government buildings across Northern Ireland, and the rest of the UK.
Loyalists have been protesting throughout the two months since the amended motion was passed.