CBA has refunded more than $8 million to 8660 customers it overcharged fees and interest on loans and also underpaid interest on savings, through its AgriAdvantage packages.

The Federal Court on Friday ordered the bank pay a $5 million penalty.

Justice Jonathan Beach said the bank failed to ensure it could fulfil the promises made to customers on the AgriAdvantage packages over a protracted period.

The failures went unnoticed for a decade.

Justice Beach said while the $5 million penalty was relatively modest given CBA's size, it should create a disincentive for large financial institutions to fail to maintain adequate processes and systems.

"I accept that a penalty of $5 million may be seen to be on the light side," he said.

"But it must be appreciated that in the present context the CBA took early self-generated steps to remedy the deficiencies and remediate its customers.

"It also reported the deficiencies to ASIC at an early stage."

Justice Beach accepted the conduct was not deliberate and noted there had been substantial and full rectification and remediation.

The Australian Securities and Investments Commission launched the civil action in March this year.

CBA quickly made complete admissions to the conduct in making misleading representations and accepting payment where there were reasonable grounds to believe services would not be provided.

CBA offered the AgriAdvantage Plus product between 2005 and 2015.

The AgriAdvantage issues were examined by the banking royal commission.

Australian Associated Press