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.
"He was flying through the air," said Mr Abraham.
The man was initially conscious but his condition deteriorated.
Train passengers were put onto buses to complete their journeys but it was expected train services would resume soon.
A spokeswoman for Veolia Transport, which operates the passenger rail network on behalf of Auckland Transport, said it was asked to close the line between Kingsland and Newmarket at the request of emergency services about 8.50am.
The company would not comment on the incident that caused the closure.