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NZTA system manager Graeme Hall said a blockage further down the drain, the responsibility of the Otago Regional Council, meant it was not yet fully clear.
However, the Otago Regional Council questioned whether there was a blockage on its part of the drain.
The NZTA said in August it would investigate claims a culvert it was responsible for was a cause of the flooding of an Outram subdivision last month.
The Anzac Court subdivision was left partly under water during July's floods, despite the possibility of flooding occurring being discussed when consent was granted in 2008.
Fred Doherty, of Outram, said at the time drainage at the site had performed well during previous heavy rainfall.
He said rusting metal at the entrance to the culvert had caused the problems.
The rusting metal was evident when the Otago Daily Times visited the site.
Mr Hall said last week the NZTA had investigated the issue.
It appeared a circular corrugated iron drain was fitted to the upstream end of the culvert, ``a long time in the past''.
"Something's come down and damaged that.''
Mr Hall said the metal partially blocking the drain had been cut off.
But it was not possible to check and clean the rest of the culvert, as there was water lying in it.
There was a blockage further down in the Otago Regional Council's drainage ditch.
A photograph from a drone showed water lying to the west of the culvert.
"Until that's cleared, we can't get in to inspect our culvert.''
The NZTA had been in touch with the ORC, and he understood it planned to clear the blockage.
ORC environmental monitoring and operations director Scott MacLean said the drain was not blocked, rather it had a flat gradient, and it was usual for there to be a small amount of water.