Rail commuters in Auckland are receiving an average of three times the subsidy of their Wellington counterparts to keep the region's trains running.
A Treasury report, released under the Official Information Act, has reviewed the current system for rail funding, and what it might mean for passenger fares.
The report says the average rail subsidy per Auckland passenger is $6 compared to $1.87 in Wellington.
Auckland Regional Council chairman Mike Lee says the differences arise partly from Auckland's rail network having been underfunded for years.
Transport Minister Steven Joyce says the issue will have to be resolved over time, but it is too soon to say what will happen with subsidies or fares.