Repairs to Wellington's rail lines are on track to be completed in time for the late-afternoon commute, KiwiRail says.
The Transport Agency said at 4.40pm traffic out of the city is "significantly congested" on State Highway 1 and 2, with queues from Ngauranga back through the the Terrace tunnel.
The motorway, all on-ramps and local roads are all impacted.
It said people should delay travel if possible.
At 7.45pm it said delays have now eased.
Wellington commuter's tales of woe in traffic gridlock
Commuters have share their wait times with RNZ this evening and some have been severely delayed.
One said they were still only half way home after an hour in a commute from the CBD that usually took 20 minutes.
Another said they've only moved 800m in 45 minutes. They said they left work at the Basin Reserve at 4.45pm and were still stuck at lights on Courtenay Place at 5.30pm.
And a commuter said they had been on the road for an hour so far from the Airport to Courtenay Place.
About 20,000 people had to find alternative means of transport this morning after a freight train derailed at a junction last night.
Details of services this afternoon would be available from MetLink, according to a KiwiRail statement.
Metlink said at about 2.30pm that it was now able to run trains on the damaged section of track. A reduced train service would run in and out of Wellington for the afternoon's peak services.
"Hutt Valley and Kāpiti line Services will resume from 4pm this afternoon from Wellington railway station and will be running to a half hourly timetable, stopping at all stations," a Metlink statement said.
WGTN TRAFFIC - SIGNIFICANT NORTHBOUND DELAYS - 4:40PM— NZTA Wellington (@NZTAWgtn) July 3, 2019
Traffic is significantly CONGESTED on #SH1 and #SH2. Queues from Ngauranga go back through The Terrace Tunnel. The Urban Motorway, all on-ramps and local roads are impacted. Please delay your travel if possible. ^CR pic.twitter.com/97AV2wKOfo
Some Wairarapa services will not be running this afternoon.
Buses will be replacing trains on both the Kāpiti and Hutt Valley lines from later this evening while crews continue to work on repairs.
Disruption will continue tomorrow as carriages need to be rearranged, and speed restrictions will be in place for the rest of the week.
Greg Pollock from Metlink told Checkpoint the cause of the derailment was still being investigated, Mr Pollock said.
He said he expected things to return to normal by tomorrow morning.
KiwiRail chief operating officer Todd Moyle said: "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.
KPL/HVL: Train services resume from 4pm this afternoon on the Hutt and Kapiti lines to half hourly timetable. https://t.co/gB8EVSY6JF— Metlink Wellington (@metlinkwgtn) July 3, 2019
"KiwiRail crews from across the lower North Island worked through the night to remove the train and derailed wagons and have today been focussed on repairing the rail lines."
Crews would continue working on the junction outside commuter train schedules to restore the network to normal operation.
KiwiRail was investigating the cause of the derailment and how to prevent similar incidents in the future, Mr Moyle said.