Three of the country's biggest banks face another drag on profits, after the regulator ordered National Australia Bank, Westpac and ANZ Bank to each hold an extra $500 million in capital until they clean up governance and cultural problems.

The Australian Prudential Regulation Authority (APRA) on Thursday said it was slapping on the extra capital requirement in response to the banks' "self-assessments" of how they managed "non-financial risks". The banks were ordered to carry out the assessments after a similar exercise at scandal-plagued Commonwealth Bank saw it get hit with a $1 billion capital charge last year.

APRA chairman Wayne Byres says more improvement is needed NAB, ANZ and Westpac. Credit:Louie Douvis

The additional charge for "operational risk," which will likely weigh on returns, will be kept in place until the banks complete their plans to strengthen their management of "non-financial risks" and close gaps identified in the self-assessments.

Managing director of White Funds Management, Angus Gluskie, said the change would lower returns slightly, in another hit to the lenders' profitability, alongside higher compliance costs and customer refunds.