Police said the pedestrian was hit by a freight train at the Papatoetoe Railway Station on Shirley Road about 6.40am on Friday.

A 59-year-old man has been killed after being hit by a train at a South Auckland railway station.

Police said the pedestrian was hit by a freight train at the Papatoetoe Railway Station on Shirley Road about 6.40am on Friday.

Police believe the man was 59 years old and are working to confirm his identity.

He was reportedly walking along the train tracks heading north towards the Papatoetoe station when he was hit by the train.

It had been a traumatic morning for the train driver and victim support had been arranged, police shift commander Tony Wakelin said.

Emergency services were at the station and it would take hours before the scene was cleared, police said.

The incident was expected to cause delays for commuters using the train network.

The KiwiRail train involved in the incident was being held at the Papatoetoe station.

A police officer at the scene said it was not known how long the station would be closed while police carried out their investigations.

Bystanders look on at the scene of a fatal collision between a train and pedestrian.

Police were talking to station security staff and getting on and off the train, which had its engine running.

Stranded commuters were frustrated at the hold up and were told by security staff to find other forms of transport or wait for the bus.

University student Sonia Ali arrived at the station at 7.30am but had to call her father to pick her up so she could catch a bus into central Auckland for university.

Sam Smith, who was waiting for the bus outside the station and expected to be late for work, said the wait was "very frustrating".

Police at the scene of a South Auckland train accident.

Auckland Transport has advised commuters on the Southern Line to find an alternate means of transport.

AT tweeted that the Southern line is blocked from Otahuhu to Homai and commuters should use buses.

Dozens of commuters who were planning to catch the train to work, school or university are anxiously waiting at the Papatoetoe station.

Most were calling friends and family in the hope of securing a ride but for some people the only option was public transport.

Customer service rep Leute Sagaga said she expected to be late getting to her central Auckland job.

Sagaga said she caught the train every day and her only other option was the bus.

Commuter Manni Singh said he had been in contact with friends affected by the delays in other parts of South Auckland who said buses were full.

Singh said he didn't like his chances of getting a seat on a bus as rush hour approached.