Although the discount had never been agreed by the council when it started last August, Councillor Kelvin Clout said it had been a gentleman's agreement.
The council decided that Pacific Hope would be charged the full commercial rate from May 1.
In another decision, a request by Marine Reach for the council to adopt the Pacific Hope was lost on a knife edge vote.
Marine Reach spokesman and Tauranga lawyer Graeme Elvin sparked a long debate when he commented on the reason why staff recommended declining adopting the ship - that the council's focus was on local community priorities.
He reassured some disbelieving councillors that adopting Pacific Hope would not cost ratepayers any money, but was a really good idea.
Mr Elvin urged the council to live up to its vision for Tauranga to have a heart and soul by not only looking inwards but to have plans and purposes beyond itself and become part of a wider world.
Supporting the move were Crs Rick Curach, Bill Grainger, Steve Morris and Kelvin Clout. Also opposed was Cr Gail McIntosh.