The highway between Pukeuri and Seven Mile Rd has closed twice for a total of six days in the past two weeks; first during torrential rain between May 23 and May 27 and for a second time on Monday night.
It will remain closed until this morning. .
The closures, particularly at Hilderthorpe, are causing increasing frustration for motorists and truck drivers.
Waitaki District Council assets committee chairman Cr Alistair Mavor is "far from amused" and said the council had raised the problem in the past.
Yesterday, agency highways operations manager Murray Clarke said work was under way on options to reduce the flood risk on SH 1 at Hilderthorpe.
Conceptual designs would be ready in three months and these would be discussed with the council and KiwiRail.
"There will also be an opportunity for those living in the Hilderthorpe area and the wider community to have their say," he said.
Cr Mavor said the agency needed to "look at the real big picture" along that section of the highway, also involving the Otago Regional Council and irrigation companies.
"We need an overall solution, not just for the state highway but also our roads," Cr Mavor said.
The worst flooding on the highway is at Hilderthorpe, just south of Hilderthorpe Rd and Lower Waitaki Golf Club, where water ponds in a dip.
It banks up across the road against the railway line embankment, but ponds on the east side of that and is unable to flow freely to a drain further south.
That portion was covered by more than a metre of water two weeks ago, taking three days to clear.
Again on Monday night, it was covered by more than half a metre of water.
Cars which tried to get through were stranded and the highway closed about 8pm, traffic again diverted along SH83 and Seven Mile Rd.
That detour puts pressure on Seven Mile Rd, causing major damage.
Yesterday, when water had drained from the rest of SH1, about half a metre remained at Hilderthorpe and the road was unlikely to reopen until about 10am today.
"The water on the highway is taking longer to drain than anticipated in an area already saturated by some of the worst flooding in 25 years," Mr Clarke said.
The agency estimated the damage from the floods to the coastal Otago state highway network at $250,000.
Most of this was for machinery and staff required to manage the floods.
The council is still assessing damage to its roads, hampered by further closures during flooding on Sunday and Monday.
Before flooding again on Monday, the council had reduced its road closure notices to seven.
That increased again to 26 on Monday, but by late yesterday had been reduced to 20.
Most of the remaining closures were due to flooding, road, bridge and culvert washouts.
Last week, the council had managed to get all water schemes back on line, but after flooding on Monday had shut Awamoko, Dunback, Hampden-Moeraki, Herbert-Waianakarua, Kauru Hill, Lower Waitaki and Windsor because of discoloured water.
Consumers on those schemes were being urged to conserve water.
