Council transport chairman cites lack of competition for the high outlays.
Auckland trains are costing almost as much as the region's buses to run, even though the buses carry almost five times as many passengers.
Council transport chairman Mike Lee is blaming a lack of competition, in which train operator Veolia had its management contract extended for more than two years in March without public notification.
Although the trains made a record of almost 11 million passenger trips in the year to June 30 - compared with 2.5 million when Britomart opened nine years ago - that cost ratepayers and the Government $105.7 million.
It was well up on $87 million for 9.9 million passengers the year before, after hefty increases in track access charges paid to KiwiRail and in Veolia's management fee.
Buses cost $110.9 million, but made 54.7 million passenger trips.
Wellington, with a simpler operating system under which KiwiRail runs electric trains as well as maintaining the tracks, spent $73 million on 11.3 million trips.
That has prompted concern from Mr Lee about the affordability of keeping his region's trains rolling, under a system involving "too many players".
The system includes large payments to KiwiRail to hire drivers for locomotives needed to haul Veolia-run trains.
Rail and bus figures supplied to the Herald by Auckland Transport represented gross costs, before being partly off-set by ticket revenue of $46 million.
Although the council transport body has been unable to provide a breakdown of that figure, it came mainly from train passengers, with the Northern Express bus service contributing most of the rest.
Most other bus operations keep their farebox takings.
Average rail trips of about 16.5km are also longer than bus rides of 6.6km, and transport planners point to the far greater congestion relief given to motorists by trains, as buses share roads with cars and trucks.
But both cost figures have alarmed Mr Lee, who is worried the growing financial burden on ratepayers may knee-cap the Auckland Plan target of doubling patronage within 10 years to 140 million annual passenger trips.
He suspects it has made Auckland Transport, of which he is a council-appointed board member, nervous on cost grounds about graduating to a 10-minute service frequency and putting on more weekend trains.
By Mathew Dearnaley Email Mathew