Ninety one per cent of all centres don't feel the fee jump is justified.
"Times are tight for centres and teachers. What we're hearing from our community and private centre members is they don't see enough value in the certification to justify the increase," council chief executive Peter Reynolds said.
"Our fear is that teachers facing a choice between paying for their own certification and staying in the industry may leave, just when we need every qualified teacher we can get."
The council called on the Government to consider alternative solutions.
This included a phased increase in teaching fee costs to lessen their impact, a proposal for the Government to fund the Teaching Council's complaints and disciplinary operation - which takes the most resource to run - so the industry could then cover the rest of the expenses through fees.
Or alternately developing the Teaching Council's ability to generate their own revenue and become self-sufficient, to lessen the financial burden on centres and teachers.
"More focus on value, efficiency and accountability would reassure the early learning sector, and should be a key element of future decision-making," Reynolds said.