The policy made little sense, given that banks were directing their customers online, she said.
"They are encouraging us to use online banking, then whacking us on the wrists."
National Bank defended its policy, saying the fee reflected the work that went into retrieving the funds.
This included "contacting the third party and getting them to reverse the payment", a National Bank spokeswoman said.
The policy was not introduced because of an increasing number of mistakes but because of the "sheer time" it took to get the transaction reversed, she said.
"We urge customers to be careful entering account details when transferring money using internet banking, and to double-check that the numbers have been transcribed correctly."
However, a survey of other New Zealand banks shows that National Bank and ANZ customers have to pay twice as much as any other bank for the same mistake.
Kiwibank, ASB and Westpac all charge between $40 and $50 to reverse payments.
Banking ombudsman Deborah Battell said she had never heard of the policy and was "perplexed" by it.
Despite this, she said the responsibility did not lie with the banks themselves.
The error was not the bank's fault, it was the customer's fault for giving wrong information.
"You can ask the bank for help to retrieve the money but ultimately it's the person whose bank account the money has been deposited into who is responsible."
The differences in fees were "up to the banks", she said.
ACC has said it will refund the $400 and the couple should have their cheque within a week - so no $100 fee payment on this occasion.
