Former staff have told three Commonwealth agencies they're missing tens of thousands of dollars in superannuation because their workplaces failed to report their allowances for postings.

Agencies are investigating the issue, telling former public servants it could cut across the Australian Public Service, and are seeking advice from the Finance Department as the owner of the bureaucracy's superannuation laws.

The Australian Federal Police, the Home Affairs Department and the Foreign Affairs Department are among agencies alleged to have left staff out of pocket.

Retired public servants say their former agencies didn't report their rent-free accommodation and hardship allowances to the Commonwealth Superannuation Corporation, which uses salary figures from employers to estimate superannuation payments.

AFP business services manager Tarnya Gersbach in an email to staff described it as a "complex issue" and said other agencies had sought advice on similar matters.

"We are seeking expert advice on the interpretation of the superannuation legislation and its application to the AFP's circumstances," she said.

"Considering the potential for broader application of this interpretation across the Commonwealth, careful consideration is required to ensure consistent treatment.

"Any impact on AFP members or former members will be managed through a separate review, once definitive advice is available."

Former and current staff from Home Affairs are also waiting for the department to finish investigating the claims.

A diabolical task awaits agencies in calculating unpaid superannuation and unpicking years of missing payments over different enterprise agreements, if investigations show they've made an error.

Retired staff claim the bill would reach into the hundreds of millions of dollars for the federal government, and say agencies have mistakenly left the allowances unreported as superannuation salary for 19 years.

The matter also threatens to complicate tax affairs for current and retired public servants.

Rules for two of the superannuation schemes covering former public servants say rent-free accommodation and allowances for housing should "automatically" be counted as salary used to calculate superannuation payments.

Allowances to compensate for hardship from posting to more dangerous and less developed overseas locations also count towards superannuation salary, former and current staff have told agencies.

An AFP spokeswoman said it had not reported to the Commonwealth Superannuation Corporation either accommodation or hardship allowances.

"The hardship allowance is not relevant for super, therefore no members are affected by the exclusion of this allowance," she said.

The AFP was reviewing how superannuation laws applied to the accommodation allowance.

"A project team has been established to undertake the review of the application of the superannuation legislation to the AFP's circumstances."

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An Australian Federal Police Association spokesman said it had held numerous discussions with AFP senior executives.

"The AFPA understands that this is a complex issue involving around 3700 members," he said.

"The AFPA was given assurances that every affected member will receive their correct entitlements and we've deliberately monitored the situation from a distance as we wanted the AFP to focus on addressing the issue with due diligence."

He said the issue was complicated by the task of identifying impacted members who had retired or left the organisation, or were on leave without pay.

The association suspected there were ex-AFP employees or people seconded to other agencies who weren't aware of the situation, the spokesman said.

The Foreign Affairs Department did not respond to questions.

The Home Affairs Department said it was working with the Finance Department and other Commonwealth agencies on the matter.

A Finance Department spokesman said agencies were responsible for managing staff remuneration and superannuation according to workplace agreements struck with employees.