Significant disruptions to Wellington's rail services yesterday have trickled into today, despite repairs to the signal system being completed overnight.

The region's train network was sent into disarray on Monday morning following a signal fault at Wellington Junction, leaving services cancelled or heavily reduced.

But KiwiRail's executive general manager of operations Paul Ashton today said specialist engineering staff had completed the necessary repairs overnight, and the signal system was working normally.

"This will allow for a return to normal timetabling but the scheduling of the resumption of services is a matter for Metlink," he said.

As of 7.30am today Metlink was still running a reduced timetable for services, which it warned would be continuing into the afternoon.

"Kāpiti and Hutt Valley Line services are now operating to a half-hourly timetable. All Porirua, Plimmerton and Taita services remain cancelled. A shuttle will be in operation for Melling to Petone. Please expect delays and use alternative transport where possible," Metlink said on its website.

Greater Wellington Regional Council spokesman Stephen Heath said now KiwiRail had discovered the fault, which was an issue with the software, they would be able to look at resuming the full timetable earlier.

They knew the commute was full and slow, particularly given other traffic woes in Wellington today, but were asking people to be patient, he said.

The painful commute packed a double whammy this morning after a crash near Tawa caused queues on the motorway.

The multi-vehicle crash happened southbound on State Highway 1 at Tawa about 6.30am, police said.

There were no significant injuries but traffic was disrupted, and police asked that motorists have patience.

As of 8.30am Waka Kotahi NZTA Wellington was advising the damaged vehicles had been removed and the road was now clear.

People could expect delays to continue, however, as queues stretched back to the Parumoana St on-ramp.

Yesterday Greater Wellington Regional Council chairman Daran Ponter said people were "literally jammed in like sardines on some trains".

Ponter said KiwiRail has flown in an expert from Auckland this afternoon who would work through the night to try to isolate the problem.

Eight railway tracks merge into two at the junction as trains approach and leave loading platforms.