They made it clear the cost would ultimately be passed to ratepayers via increased sums they will charge Auckland Transport for their services.
Auckland Transport said costs would be "incurred through new contract rates".
Birkenhead Transport owner Robert Inwards must find $500,000 to paint 75 buses, and would pass that to Auckland Transport.
"So at the end of the day the ratepayer will pay for it."
Ritchies owners Andrew Ritchie has 180 buses affected.
"It will be in the millions [across the fleet] ... I wonder how a coat of paint is going to change patronage?"
Bayes Coachlines owner John Bayes said Auckland Transport told him to add the cost of painting his 20 buses into his next contract.
Howick and Eastern general manager Sheryl Otway said 150 buses would be affected and she "assumed" the cost would be factored into future contracts.
NZ Bus, which has 700 buses on Auckland Transport contracts, declined to comment.
Auckland Transport said on Thursday the change would take place over the next three years. However, the organisation's spokesman Mark Hannan could not say before deadline how many buses would be repainted and how much it would cost.
Bus company owners believed most of their fleets would be affected, but Auckland Transport said costs would be kept to a minimum by keeping rapid network, link and Airbus buses the same colour.
Hannan said most repaints would be targeted to occur when buses were replaced or due for repainting.
An unknown number of older buses would be exempt and operator names would remain on the side of all buses.
Auckland Transport general manager for marketing and customer experience Mike Loftus said a single identity would give patrons a clearer understanding of what public transport was available and which areas they served.
The organisation's group manager for public transport, Mark Lambert, said a single public transport network would increase use, which was part of The Auckland Plan's goal of doubling public transport trips from 70m in 2012 to 140m in 2022.
Some bus operators said Auckland Transport also told them upholstery and uniforms were part of the changes, but Hannan said no decision had been made about.