The reduced train services and bus replacements are likely to increase traffic congestion and commuters are being urged to prepare for this.
Some services may also be cancelled.
"The track damage means no trains will be able to run between Petone and Wellington until repairs are completed," said Tranz Metro manager Scott Brooks.
Mr Brooks said staff have been working around the clock since the storm to ensure repairs are completed as quickly as possible
However, in some places support structures have been completely washed away and would take some time to be repaired, he said.
KiwiRail's Chief Executive, Jim Quinn, said the storm damage is unprecedented.
"We had track so undermined it was literally hanging unsupported. Overhead poles were damaged at their foundations. Debris and ballast covered the lines."
"Realistically, we're unlikely to see services restored on the Wairarapa-Hutt Valley Line until the end of the week."
NZ Police Hutt Valley Area Inspector Mike Hill is urging commuters to consider carpooling if they decide to travel by car into Wellington City.
A special half hourly timetable will run on the Hutt Valley Line with trains running between Upper Hutt and Petone.
All train services between Petone and Wellington will be replaced by bus until further notice.
Tranz Metro has a special timetable for the Hutt Valley Line and the Wairarapa Line on their website and is urging customers to check the website before they travel at www.tranzmetro.co.nz.
Mr Brooks said Tranz Metro will continue to update customers but for the foreseeable future customers should use the timetable to make travel plans.
The effects of the storm have been felt widely across the region with councils organising clean ups. Parts of Cape Palliser Road were closed over the weekend due to falling rocks, and high seas causing washouts. On Sunday, Kupe's Sail to Mangtoetoe (between Ngawi & The Light House) was still closed.