One worker raised the alarm, and now AFP faces a $22m bill for super

The super bungle could impact as many as 3700 past and present federal police employees across Australia.

The federal police has admitted to not paying superannuation on certain employee allowances, but insisted the mistake was "not a conscious omission".

The Australian Federal Police Association wrote to commissioner Andrew Colvin in late July requesting an investigation into employee superannuation, after one of its members raised concerns about how payments had been calculated.

The complex matter stems from the terms of a 2007 enterprise agreement, which expanded the types of employee allowances that were eligible for superannuation purposes, including nightshift and overtime.

Under the previous agreement, superannuation was only paid on higher-duties allowances for federal police employees.

Since the oversight was discovered, the federal police has been pouring over its records to determine how many past and present employees have received incorrect superannuation payments.

The AFP this year included a $22.3 million correction in its 2017-18 annual report to account for possible back payments.

In a statement to Fairfax Media the AFP said that figure was a "high level" estimate of the scope of repayments.

The statement said that initial estimates had indicted about 3700 employees had been underpaid.

"Given the nature of the allowances and the complexity of superannuation a large number of employees are potentially affected," the spokesman said.

"Due to the complex nature of the adjustments required, the correction process will take some time to work through each member's individual situation."

Fairfax Media understands the federal police began emailing employees who might be affected by the oversight last week.

The Australian Federal Police Association acting president Graeme Cooper said there was no suggestion the federal police had knowingly avoided payments.

"We are satisfied that the AFP have reacted to this issue in a deliberate and methodical way," Mr Cooper said.

"Superannuation is a complex matter and having to re-examine the payment records of all employees to establish whether they are affected is time consuming."