The council used a targeted differential rate for rural properties and lifestyle blocks to collect the funds but wanted the board to take it over.
But Animal Health Board chief executive William McCook said the board relied on the funds to carry out its work in the area.
"Any cut to the regional council's contribution would have an impact on these other funding sources and seriously compromise efforts to eradicate TB from the region."
Mr McCook said there had previously been a lot of public support for the funding to be included.
The number of infected cows with TB has dropped significantly in the Waikato. There were 17 cases of infections in 2008 and two in 2011.
Waikato Federated Farmers president James Houghton said he would be opposing the proposed cuts and had concerns about an increase of TB in livestock and access to international markets.
"The regional money helps get the national money so without their money we have the potential to lose a lot of services required in that area."
Mr Houghton said it was disappointing Waikato was the only regional council to back away from the deal. "I can't understand where they are coming from, AHB pays them to collect the money so what is the issue."
Upper Coromandel Landcare Association spokeswoman Riehana Robinson said the move was hypocritical.
"Claiming that AHB pest control suddenly is not core business while handing out $6 million of cold ratepayer cash for an elite cycle track is outrageous. Ratepayers should be funding neither."
The relationship between the council and the AHB appears to have been strained since the board took back management of the programme three years ago. The council withdrew funding in 2008 only to reinstate it the following year.
The council will consider the cuts next week.