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Mr Brownlee offered his resignation as Transport Minister, but that was swiftly rejected by the PM.
"Running late for a plane this morning, I took a door that is normally used for an exit at Christchurch airport onto the forecourt ... and you're supposed to go through airport security," Mr Brownlee told reporters this afternoon.
He said he did not give it any thought, but has now apologised unreservedly for the action.
Mr Brownlee only offered his resignation after he was contacted by Aviation Security.
"I didn't initially consider that it was a huge problem. [Only after a phone call from Aviation Security] I suddenly realised, 'Hell, this is a pretty serious matter'.
"I should have known. There's no question, that's why I've offered the resignation."
He denied telling an airport staff member at the exit door that "the rules had changed".
"I had two other people with me. There was no way I said that.
"I really don't want that guy getting in trouble. It was all my fault ... I made a stupid error and I deeply regret that.
"My words were: 'We're in a hurry to get on the plane. Can we shoot through here?' In the end he let us through, but it was all my fault, no one else's."
Mr Key said he was disappointed in his Transport Minister.
"Gerry knows better than that and while he was obviously in a hurry, lots of people are in a hurry and that's not an excuse, and he doesn't accept that as an excuse,'' Mr Key said in Christchurch today.
"He's offered his resignation and I've decided, on balance, not to accept his resignation. In making that decision, I considered the whole matter very seriously.
"But I had to weigh up all of the tremendous things he's done in the six years he's served as a minister.
"He's made a stupid mistake. I'm absolutely confident he'll never repeat that again.''
Events played out very quickly today, with the incident, Brownlee's admission and apology, and offering his resignation, which was turned down immediately by the Prime Minister.
"[Brownlee] has obviously got off the plane and taken a second to reflect on what has happened. While he hasn't intended to put himself in this position, he has put himself in this position and he's immediately realised the severity of what he has done and he's offered his resignation.
"I could take a long time to consider the matter. I sought some advice on it but as you would expect, relatively quickly I needed to respond, and that's why I made the decision now.''
He said that Mr Brownlee had "fessed up straight away, unreservedly apologised and unreservedly taken responsibility''.
"In the history of Parliament, we can point to other ministers in previous governments that haven't necessarily taken responsibility for actions like this. It doesn't make it any better, and it certainly doesn't make it right,'' Mr Key said.
"I'm very disappointed in Gerry and I know he's deeply disappointed in himself.
"No one's offering excuses - I don't think there is a reasonable excuse to offer. All I can say is I have to consider whether six years of incredibly hard work should all be washed away because of one really silly action. I think, on balance, it shouldn't.''
Asked if Brownlee was charged over the incident, would he consider changing his decision, Mr Key replied, "No one is above the law. If he is subject to the law, and if he's potentially fallen foul of that, then he'll have to face the consequences of that like anyone else would.''
But he wouldn't consider changing his mind if charges were laid, saying he would rather wait and see what happened.
Labour MPs mocked Mr Brownlee during Question Time in parliament today.
Clayton Cosgrove asked if Mr Brownlee's airport antics was a pilot project into running.
Mr Brownlee replied he was in favour of running for its health benefits, but not political benefits.
Mr Brownlee said he felt "very lucky'' to continue to have the Prime Minister's support.
"I hope it doesn't cause any further disruption to his plans over the next short while.''
He said he may have missed his flight if he had not have gone through the exit door, but he was unsure.
"The plane was boarding and our boarding passes were in the gate lounge waiting for us.
"We were coming up from the regional lounge toward the normal security way. There was another way that is normally used as an exit. That was open, and I went through there and ended up in the gate lounge.''
Labour's transport spokesman Phil Twyford did not want to say whether Mr Brownlee should keep his job.
"Gerry Brownlee should be subject to exactly the same consequences for this breach of aviation regulations that any other New Zealander would be.''