Auckland rail commuters are receiving an average of three times the government subsidy for the region's trains compared with passengers in Wellington.
A Treasury report released under the Official Information Act reviewed the system for funding rail and what it might mean for passenger fares.
According to the Treasury, the average rail subsidy per passenger is $6 in Auckland and $1.87 in Wellington.
Auckland Regional Council chairman Mike Lee says the differences arise partly from Auckland's rail network having been under-funded 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 to subsidies or fares.