Instead of running in both directions for seven days a week over summer and three in the off-season, trains will leave Auckland on Mondays, Thursdays and Saturdays and return from Wellington on Tuesdays, Fridays and Sundays throughout the year.
The plan is opposed by communities along the way, from which 8073 people have signed a petition to keep the stops.
Mangaweka art gallery owner Richard Aslett, representing Rangitikei District Council's Taihape ward, said it would hurt provincial New Zealand for no great advantage to tourists.
Those needing to travel between Auckland or Wellington in a hurry would keep catching aircraft, leaving those with more time to take the train.
"People getting that train are not bothered by an extra hour and a half - a lot of them would prefer to be on there longer, the train enthusiasts," he said.
But KiwiRail passenger services general manager Deborah Hume produced a table recording average patronage ranging from 0.2 to 3.7 passengers at stops to be axed.
Despite attempts to make the Overlander service more attractive, annual patronage fell from 72,881 passengers in 2009-10 to 51,650 last year - a 29 per cent drop to 111 people on each train - for an "unacceptable" daily loss of about $9000.
That followed an increase from 47,119 in 2007, after a campaign by the former Auckland Regional Council and three others persuaded previous operator Toll Holdings not to abolish the Overlander.
Ms Hume said that if groups of 10 or more passengers wanted to get on or off at a smaller stations along the way, trains would stop there.
"And should the provincial regions grow passenger numbers and tourist attractions, we would be willing to look at reinstating stops."
Herald reader Kathryn Arnold said the old Silver Fern railcar managed to travel between Auckland and Wellington more than 20 years ago in 10 hours and 10 minutes while still managing 14 stop along the way.
FOR THE CHOP
Middlemore, Papakura, Pukekohe, Otorohanga, Te Kuiti, Taumarunui, Taihape, Marton, Feilding, Levin, Paraparaumu, Porirua.