Passengers on the 4.02pm Southern Cross to Bendigo service were told the train was "running out of fuel" and would need to terminate at Kyneton station.

Long-time V/Line commuter Sarah Harris said the conductor told passengers the train was "running on one engine".

"I've never known such a thing to happen before," Ms Harris said.

"It would have sounded more plausible if they said bunyips had ripped up the rails.

"It slowed down so much, by the time we got into Kyneton a couple of people joked we would have to get out and push." 

A V/Line spokesman confirmed the train terminated at Kyneton, saying the fuel issue was due to a faulty light.

"A low fuel light failed to activate and one of the three diesel engines on the train shut down," the spokesman said.

"The train continued at reduced speed to Kyneton where coaches were provided for customers to continue their journey."

Ms Harris, who boarded a bus in Kyneton, said there was about three carriages full of people.

In 2011, rail passengers in Melbourne's west experienced delays of more than an hour after a V/Line train ran out of fuel and blocked the lines.

V/Line apologised to customers for the inconvenience.