There are no reports of injuries, but passengers said they could hear the rocks hitting the trail while going from Paekakariki and Pukerua Bay.
RNZ's Todd Zaner was on the carriage that was struck, and says it was pouring with rain when he got on at Paekakariki. The train got through a tunnel and abruptly stopped.
The driver announced there were rocks on the track - and then a series of rockfalls hit the carriage.
The driver and another staff member ran through the carriages and reversed the train away from the rockfalls, back to Paekakariki station where commuters got off.
Meanwhile, a lane on State Highway 2 through the Hutt Valley has been closed.
Heavy rain warnings were in force Monday morning for the lower North Island, as the weekend's wet and boisterous north-to-westerly winds continued.
A heavy rain watch was in place for Horowhenua Kapiti Coast, and the Wellington area, including north of Porirua and Upper Hutt, set for between 5am and 5pm. MetService warned of "periods of heavy rain, and amounts may approach warning criteria.
An orange warning was already in place for the neighbouring Tararua Range, with up to 120mm of rain expected, possible thunderstorms and the chance it could be upgraded to a red warning.
NZ Transport Agency/Waka Kotahi this morning warned motorists in the area to "drive according to the conditions - wet roads are slippery, reduce speed, increase following distances, avoid sudden braking, and use headlights if visibility is poor".
Localised flooding led to a northbound lane on SH2 near Petone being closed.
Bad weather was also affecting driving conditions on SH1 from Wellington to Levin and SH58, Haywards Hill to Pāuatahanui and Pāuatahanui to Judgeford.
