Leaked documents throw into question a controversial decision to dump electric trains for diesel locomotives between Hamilton and Palmerston North.
KiwiRail announced the decision last year, and said diesel would improve reliability and efficiency.
But an external peer review by engineering consultants WorleyParsons warns diesel trains bought from China have "a very high failure rate".
Seven to nine are out of service at any one time for maintenance, repair and asbestos removal. And their performance has been "extraordinarily poor".
The review said KiwiRail should be switching its whole fleet to electric, but it said a paper from the company’s board was "biased towards the diesel option".
And there are more concerns from a separate internal report, which says KiwiRail over-inflated expected savings – and upgrading electric trains was actually $230m cheaper than replacing them with diesel.
And Treasury also had concerns. Cabinet advice given to the Green Party under the Official Information Act shows officials weren't convinced by the business case.
They warned KiwiRail "provided no basis for its cost estimate" that electrifying the whole main trunk line could be up to $1bn.
The electric trains will be phased out in the next two years. But Transport Minister Simon Bridges says the whole line could be electrified in the future.
"There is an avenue down the line for different decisions to be made ... we can revisit this in due course - if we decide that's the right thing to do," he said.
But critics say the weight of evidence shows the right decision is not diesel.
Green Party transport spokeswoman Julie-Anne Genter said it is "shocking" that KiwiRail chose the diesel options. She wants Mr Bridges to call a halt to the plan - and commission a full independent report.
The Greens want the existing electric trains upgraded - and the entire trunk electrified over time. Ms Genter says the reports show that's the best value for money.
KiwiRail says the reports were written in 2015 - a year before it made a final decision.
Chief executive Peter Reidy says there were three or four reviews.
"It matured all the way through, so the initial information that we were looking at at the start looked very different towards the end," he said.
"It's not our job to cook the books - we are very comfortable that this is the right decision for our business."