The barriers were down and warning bells were sounding at the time.
The train driver saw the man and slammed on the brakes and sounded the horn "but unfortunately struck the pedestrian'', Mr Abraham said.
"I believe he was wearing headphones, listening to an iPod so he wouldn't have heard the second train.''
The man was knocked to the side of the tracks, where passengers saw him lying after the train came to a standstill.
Passengers were put onto buses to complete their journeys and train services resumed at 10.30am, said Michelle Roach, a spokeswoman for Veolia Transport, which operates the passenger rail network on behalf of Auckland Transport.
All drivers involved in accidents are offered counselling and stood down for the rest of the day. A blessing was carried out on the train following the accident.
The incident is one of several where people have been killed or injured while listening to musical devices.
New Zealand Transport Agency spokesman Ewart Barnsley said they strongly recommend pedestrians stay aware of their surroundings at all times.
"That would certainly apply if you're out walking and you can't hear a train signal.''
Mr Barnsley said music shouldn't be so loud that it drowns out any warning sign.
Earlier this month a 17-year-old Korean student suffered serious injuries after she was hit by a car in Auckland while wearing an iPod, said police.
Mt Maunganui woman Kumiko Wakamiya Goodhall, 55, was hit by a train in Tauranga in April 2010. She was listening to an iPod at the time, which police said may have prevented her from hearing the warning bells and the approaching train.
Gareth Hotham, 30, also died after he was struck by a train while wearing an iPod in Te Puke in November 2009.