Although both operations provided around 11.5 million passenger trips in the 12 months to June 30 last year, subsidies paid for each kilometre per patron in Auckland amounted to 65c, compared with the capital's 16c.
Fares contributed 22 per cent of Auckland's operating bill of $139.3 million, compared with 50 per cent of Wellington's $85.1 million.
Mr Lee said in May the extra burden of a $114 annual transport levy on Auckland households meant the council had "a moral obligation to make sure we are getting value for money".
In his report, which goes before councillors tomorrow, Mr Callow highlighted variations in services as the main reason for the cost differential.
"Auckland operates a comprehensive timetable with every train stopping at every station, whereas many of Wellington's peak services only stop at half the stations and cover half the line."
He said the duration of a train run in Auckland was typically one hour, compared with 20 to 45 minutes in the capital.
Yet a large number of short one-stage trips were taken into Britomart on Auckland trains, costing just $2.50 cash (or $1.70 by Hop card), compared with Wellington, where journeys on the busiest two lines to its central railway station were at least three stages - for a minimum of $5.50.
Other considerations included more "dead running time" to reposition trains in Auckland and higher maintenance costs for old diesels which have since been largely replaced by an electric fleet.
Mr Callow said staffing practices on trains in the two cities were broadly similar.
But when adjusted for the other factors, costs of running each Auckland service were only about 10 per cent higher than Wellington's.
He expected that difference to vanish once Auckland's fleet of 57 new electric trains became fully operational in coming months.
Mr Lee said he believed a major reason for Auckland's rail labour costs amounting to $43.2 million, compared with Wellington's $25.4 million, was the large amount spent here on roving ticket inspectors rather than having on-board staff checking fares.
He said patronage had risen 22 per cent in the past year, to 14 million passenger trips, yet fare revenue was just 16 per cent higher.