Companies will have to pay new levies to the Financial Markets Authority, External Reporting Board and the Companies Office from August.
Commerce Minister Craig Foss says the levies will provide $16 million in annual funding for the FMA and nearly $4 million for the board.
The levy will be a tiered system where different market participants pay differing amounts, according to their size.
Banks say they are being unfairly lumped with disproportionately high levies to fund the FMA.
The four big banks will pay $350,000 each per year - together contributing about 8.5% of the total levies.
Other banks and finance companies will pay levies ranging from $2000 - $80,000, based on the size of their assets.
The Bankers Association says the industry has no problem contributing to the FMA's costs, but the current setup means banks are effectively paying for poorly-run failed finance companies.
Chief executive Kirk Hope says banks prefer a model whereby all registered companies and trusts pay a much lower flat fee of $40 each.
"Banks are already very regulated entities through prudential regulations, so we don't necessarily agree with the assumption that the banking industry gets significant benefit from this regulation to be honest", he says.
Mr Hope says all companies will look to access capital at some point in time, so they are probably getting the biggest benefit from a well-regulated market.
The levies will be reviewed in two years, and in the meantime Mr Hope says the organisation will keep talking about its concerns with the Government.
Mr Foss says the tiered levy system was finalised following a thorough consultation period, and he's confident it has struck the right balance.