Meanwhile the Melling services are cancelled and Johnsonville continues to run as usual.
The capital's roads were thrown into chaos this morning thanks to a freight train that derailed near the central city last night, damaging crucial sections of track.
The derailment means most of the region's train lines weren't running this morning as commuters tried to make their ways to work.
Meanwhile, a number of bus services have been cancelled for this evening's commute.
• Bus 24, 6.45pm Johnsonville to Miramar Shops, cancelled.
• Bus 25, 4.20pm Khandallah to Highbury, cancelled.
• Bus 24, 7.45pm Johnsonville to Miramar Shops, cancelled.
• Bus 24, 9.10pm Miramar Shops to Johnsonville, cancelled.
• Bus 24, 10.45pm Miramar Shops to Johnsonville, cancelled.
• Bus 25, 5.20pm Khandallah to Highbury, cancelled.
Some services on the Wairarapa line will not be running this afternoon.
The 5.30pm Wellington to Masterton service has been replaced by bus, departing Wellington at 5pm.
The 6.18pm service from Wellington to Masterton will be a train service all the way from Wellington to Masterton.
About 20,000 train commuters scrambled to find a way in to the city this morning, with not enough replacement buses to carry everyone.
There is heavy congestion on the roads and people are being asked to delay travel.
In a statement, TAIC said it had opened an investigation into last night's freight train derailment.
"Circumstances reported to date are that the loaded train was travelling out of the Wellington Rail yard when it derailed at the junction between the yard and the North Island Main Trunk line.
"Four wagons are reported to have derailed. There were no reports of injuries."
A team of investigators had been appointed and were working at the scene today.
The Commission said it opened an inquiry when it believed the circumstances of an accident or incident could have "significant implications for transport safety, or when the inquiry may allow the Commission to make findings or recommendations to improve transport safety".
Eight sets of points - which allow trains to switch tracks - and sections of track were damaged on Tuesday night when four container wagons on a freight train derailed at the junction as it was leaving the Wellington Rail Yard.
The rail lines were closed from about 7.40pm.
KiwiRail crews from across the lower North Island worked through the night to remove the train and derailed wagons and have today been focused on repairing the rail lines.
The crews will continue to work on the junction at night over the course of the week, to fully restore the network to its normal operation. This will be done when commuter trains are not operating.
KiwiRail is investigating the cause of the derailment and how to prevent similar incidents in the future.
'Hunger Games' for bus users: councillor
Greater Wellington regional councillor Daran Ponter told Newstalk ZB this morning those who live in Hutt Valley and the Kāpiti Coast should consider staying home.
"A freight train has taken out the signalling in the choke point in the Wellington rail yard."
It's the place where all the trains are coming into the city, he said.
"I'm afraid for those people who are relying on buses it is going to be a little bit like the Hunger Games out there."
Ageing infrastructure to blame
Greater Wellington Regional Council chairman Chris Laidlaw said today's chaos was "a failure of our KiwiRail system".
"It's a product of, I suspect, ageing infrastructure.
"We depend crucially on that Government-owned infrastructure to make the system work."
Laidlaw said there had been "quite a lot of money" dedicated to upgrading the network in the rest of the region, but more needed to be done in the central city.
"This has happened before and it will happen probably again until the KiwiRail asset is upgraded."
Laidlaw also asked people to understand why there were not enough replacement buses.
"Look, there is no large pool of buses held in reserve sitting and waiting at the depots. The bus companies don't do that and you can understand why."
The Wellington Chamber of Commerce said the train problem was a wake-up call to the Government and councils.
"We are stuck with narrow corridors thanks to being squeezed between the hills and the sea, so our infrastructure must be resilient to all eventualities," a spokesman said in a statement.
"We have a limited number of roads and rail lines, and when something happens to them then this sort of chaos is the result.
"The real problem is that the Government has deferred solutions till well into the future.
"Let's Get Wellington Moving and the Petone to Grenada link are prime examples of this.
"Businesses and the public made it very clear what they needed and expected from the Let's Get Wellington Moving project, but they're not getting the big parts of it for many, many years.
"We need the two tunnels and the grade separation at the Basin as soon as possible, not in 20 or 30 years.
"The Petone to Grenada link would have made a big difference today but that's been put on hold till the end of next decade, so that part of the transport network remains vulnerable, as we also saw earlier this year with a slip on Highway 2.
"The rail corridor is clearly also inadequate and needs more serious investment to make it more resilient."
The New Zealand Transport Agency is encouraging commuters to leave work before 3pm or after 6pm to help with congestion today.
There may be disruptions during tomorrow morning's rush hour as carriages need rearranging, but Metlink will be doing everything possible to return to a regular timetable.
There are likely to be speed restrictions for the rest of the week, creating delays in and out of Wellington on the affected lines.
Updates on the trains can be found on the Metlink website.
Meanwhile traffic is already starting to build, and a crash on SH1 near Johnsonville is adding to the congestion.
