The decision was made in 2014 to launch a "consistent brand" across Auckland's buses, trains and ferries under the Regional Public Transport Plan.
Auckland Transport spokesman Mark Hannan said the designs for the ferries were not finalised but their "current thoughts" included a white base with the AT Metro logo and the vessels would be joint-branded.
Costs and details are yet to be finalised, Mr Hannan said, but it would form part of the tender process over winter.
Karen Goa, organiser of a campaign to halt the painting of the 75-year-old beige Birkenhead Transport buses, was outraged at the decision to "joint-brand" the ferries.
She questioned how AT could justify "slapping a logo" on ferries that were already white while buses needed a completely new paint job.
On behalf of almost 2500 people, she submitted a petition to AT.
Councillor Christine Fletcher has assured Ms Goa it will be tabled at the next meeting.