Liam Mason, director of regulation at the FMA, said the regulation had been in place for more than three years.
"Firms and individuals have now had sufficient time to meet the legal requirements.
"We have taken proportionate action to ensure all reporting entities are clear about their obligations under the law."
The FMA said it chose not to name the 12 companies and individuals as there were either small businesses or individuals and naming them would have had a disproportionate effect.
All nine of the companies who failed to provide an audit were now taking steps to do.
The FMA said it would be taking further steps against the two reporting entities who didn't respond to its requests and the single reporting entity that failed to provide its annual AML/CFT report if they fail to respond to its warnings.
Mason said independent audits were an essential component of complying with the Anti-Money Laundering and Countering Financing of Terrorism Act to help ensure reporting entities have robust systems and processes in place.