Both highways were vital routes in and out of the region. Every time snow closed State Highway 1 (the Desert Rd), trucks used SH4 and SH3 as alternatives.
The region had enjoyed one of its best summers in a long time but still the roads were nowhere near up to standard.
The onset of winter would affect the amount of work that could be completed, Mr Cloke said.
"Our real worry is that SH4 is vulnerable already and always has been.
"If there's another weather event like last June, we'd be lucky to hold that road in place at all. The Parapara is open, but traffic is restricted where washouts have occurred. It's the incessant stops and starts which are affecting productivity and costs."
Steve McDougall, chief executive for McCarthy Transport in Whanganui, said the longer repairs took the more it was costing his company.
McCarthy trucks use the road every day, especially logging trucks.
Mr Cloke said the NZTA had now agreed more cosmetic work would be done immediately to help overcome some of the issues while work on the more major problem areas was also being considered.
He said the agency would write to the RTA with a more detailed outline of its work programme for the route, and they expected to have that information in the next couple of weeks.
Earlier last month, NZTA said efforts were being made to speed up repairs but the work might take two years.