Flightline Aviation helicopter service manager Pete James said more than 6cm of floodwater covered the concrete floor of the company's hangar on Saturday morning.
Nearly 30 helicopters inside got ``wet feet''.
The floodwater did not enter the office space.
``We got away with it lightly.''
However, the underground tank containing aviation fuel remained underwater yesterday.
An alarm sounded yesterday, warning the fuel could have been contaminated with water.
Jonathan Hill, a spokesman for Z Energy which owned the tank, said the site would be checked when the floodwater receded.
He hoped the investigation could start today.
``The site is closed, so there is absolutely no cause for any safety concerns.''
Mr James changed windows on an MD 500 helicopter yesterday as ``some of the boys'' swept out the hangar.
``They got a lot of the mud off the floor, where the water had receded.''
The greatest concern over the flood was the sewerage system at the airport failing and sewage entering the hangar.
Dunedin Airport chief executive Richard Roberts said the sewerage system was coping after the flood and no sewage had overflowed from it.
