The Australian Securities and Investments Commission (ASIC) on Thursday said it has started Federal Court proceedings over the failings from the mid-1990s to September 2021.
Customers of ANZ's `Breakfree' package paid an annual fee to be eligible for waived fees and reduced rates on home loans, transaction accounts and credit cards.
The bank did not always do so and has been paying customers almost $200 million in compensation.
ASIC deputy chair Sarah Court said the conduct was long-standing.
"These customers were entitled to receive the benefits they signed up for and in many instances paid for," she said.
"This case is yet another example of a widespread system failure by a major bank impacting thousands of customers."
This is the final ASIC investigation into failings uncovered by the Financial Services Royal Commission, which concluded in 2018.
ANZ will not contest the court proceedings and has joined ASIC in proposing a fine of $25 million.
The bank said it has improved its systems and apologised to customers.
ASIC has not claimed the benefits were withheld deliberately.
The bank will pay the last of the compensation in the 2023 financial year.
Shares in the bank were little changed at $27.65 at 1127 AEDT.
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