Auckland Transport owns the stops with no advertising and repairs all damages other than graffiti, which the council pays to remove with its budget, and Adshel owns and repairs all the stops with advertising.
Since July 1, 2013, ratepayers forked out almost $2 million repairing more than 2220 stops belonging to the council or Auckland Transport, while Adshel was forced to repair almost 3500 between 2013 and 2015 at a cost of $461,000.
However, despite the huge cost, Auckland Transport only knows of six people held responsible for the vandalism but charges are not always relayed to the agency by police.
Despite smashed glass requiring the most clean-ups, at an average of $350, Auckland Transport reinstalled glass instead of tougher materials because they had to meet safety standards, said spokesman Mark Hannan.
Glass aids visibility of what's happening in the shelter both from passing traffic and CCTV so they needed "compelling reasons" to use another material, Mr Hannan said.
Mr Hannan said Auckland Transport's records of how many people were held responsible might not reflect the actual number charged by police as sometimes the agency is not notified.
"Of course we would like to see more people charged but these incidents tend to happen when there are not people around and at stops not covered by CCTV."
Senior adviser for graffiti vandalism prevention at Auckland Council, Rob Shields, said when a vandalised stop is brought to the council's attention, private investigators are then sent, through the Auckland Graffiti Vandalism Prevention Plan, and they gather information and evidence relating to active graffiti vandals in Auckland.
They then pass the information on to police.
Adshel's New Zealand general manager Nick Vile said they considered vandalism a cost of the business.
"We would of course prefer it didn't happen but we factor it in as an inevitable cost."
At stops which are hit more often, the advertising business has installed metal-netted panels in place of glass.
Three most attacked stops since 2013:
• 6571, 79 Mangere Rd - 11 times
• 6312, 42 Flat Bush Rd - 10 times
• 4033, 243 Rangatira Rd - 10 times