A Kiwirail spokeswoman said 225 of the 366 passengers on the 6.21 service travelled by bus.
Remaining passengers waited for train engines to be switched over, at which point a seven-car train continued to Wellington.
Commuter Marc Rebus said delay at Featherston of more than an hour was frustrating.
"It was pretty chaotic, communication was terrible - no one really knew what was going on," he said.
"We were first told it was a driver issue, which turned out not to be the case ... you could feel time ticking away, and seeing people get agitated as they became later and later."
Another passenger, who did not wish to be named, said passengers were confused.
"No-one was taking charge, giving instructions ... they've got a PA system, so why couldn't they use it?"
Despite the confusion, passengers said they were pleased with Tranz Metro's text-warning system, which let them know about the breakdown.
Kiwirail said the company had not received any complaints of confusion.
Train fare increase, p3