The Director of Civil Aviation, Graeme Harris, confirmed the alleged security breach.
"The primary focus for the CAA is to determine the facts of the incident and take action to prevent something like this happening again."
It remains unclear what law or rule may have been broken. A security area breach can only apply if the person refuses to identify themselves, or refuses to leave if asked by a security officer.
The law contains a general trespass offence but it cannot apply if permission to be there was granted - which Mr Brownlee claims it was.
Mr Brownlee has delegated the aviation security aspects of his portfolio to Associate Transport Minister Michael Woodhouse.
If passengers board a plane without being screened, the plane and departure lounge are meant to be cleared and everyone should pass through security again.
Mr Brownlee said he would fully co-operate with the investigation.
The Prime Minister said he was "very disappointed", but it was not a sackable offence.
For the Herald's full coverage of the 2014 election: tinyurl.com/nzhelection
additional reporting: Kurt Bayer