The claims, backed in part by Fair Work Ombudsman findings and a repayment, mean half of Canberra's eight Crust Gourmet Pizza Bar stores and four different ownerships have been found to have underpaid their staff.

In addition, a quarter of all requests for assistance from Crust employees to the Fair Work Ombudsman have come from the ACT, the industrial watchdog said on Friday.

The long-term workers, who both parted ways with Crust late last year after at least four years each in ACT stores, said the alleged breaches were a structured part of the franchisees' business.

One, an employee who worked at Kingston, said that drivers were paid cash as standard throughout his time there, missing out on penalty rates and superannuation. There was a "big push to put everyone on the books correctly" after Fairfax Media revealed underpayments at the Gungahlin store last September, he said. The Gungahlin issues triggered a call by UnionsACT for an independent audit of every store in the chain.

The new Kingston claims came as a separate former employee revealed a Fair Work Ombudsman investigation completed last year found the then-Erindale franchisee owed him $14,700 for unpaid weekend and night penalty rates and casual loading, contravening federal industrial laws. The underpayments related to a 2.5 year period to late 2013.

The same worker was repaid another $3500 last year for similar types of underpayments for later work at the Conder store.

Working as an assistant manager at Conder and during the final months at Erindale, he said drivers were paid cash only and not given their full entitlements.

The Erindale and Conder franchises were held by the same owner, who has since sold all interests in Crust stores. There was no comment from the former franchisee this week.

Fairfax Media does not suggest wrongdoing at Erindale or Conder by the current franchisee, understood to be SAI Hospitality.

The former Erindale employee said moves to put staff on the books while he was at the Kingston store last year "never actually went through because most of the drivers didn't want to because they all had second jobs, then they'll pay more tax."

Crust's Kingston store acknowledged earlier this month that there were underpayments in relation to two drivers in the period since November last year, when SAI Hospitality took over that franchise. It had been alleged all drivers were getting paid in cash and missing out on entitlements. Retail Food Group, who own the Crust franchise system nationally, said the majority were found to have been paid in line with the award.

The Gungahlin Crust store management agreed last year to compensate many workers, both drivers and in-store staff, for underpayments, and to end the cash-in-hand model used.

There was no response from the immediate past franchisee for the Kingston store, Chris Felemegas, this week. Fairfax Media understands he retains no Crust ownership interests.

His brother, Peter Felemegas, who works at the Braddon Crust store owned by his wife, confirmed the national headquarters had sent through emails last September directing all franchisees to put all workers on the books, with warnings franchises could be lost if there was not compliance.

He said business was hard in Canberra, with too many shops generally, and industrial awards were "too generous". Fairfax Media does not suggest any underpayment at the Braddon store.

A Fair Work Ombudsman spokeswoman said the Ombudsman had received 46 requests for assistance from Crust employees throughout Australia, including 11 in the ACT, between July 2011 and the end of March. ACT stores make up only five per cent of the 167 Crust shops operating nationally.

Nationally, allegations by some employees were not substantiated, with others resolved by the parties themselves and some with the Ombudsman's assistance, and some back-payments occurred.

"There were a number of enforcement outcomes, including the issue of Compliance Notices, Infringement Notices (on-the-spot fines) and Letters of Caution," the spokeswoman said.

Retail Food Group, who own the Crust franchise system, responded to questions about its oversight in similar terms to questions a month ago, and made no specific mention of the Erindale, Conder or Kingston stores.

"While employment arrangements with team members are ultimately the responsibility of franchisees, as soon as Crust is made aware of any instances of underpayment of team members, those allegations are immediately investigated and promptly resolved," a spokeswoman said.

"Crust fully supports any team members, past or present, in seeking their full entitlements from their employer.

"Crust considers any instance of non-compliance with obligations to be unacceptable, contrary to the brand's values, and inconsistent with the standards set for franchisees."

A Fair Work Ombudsman audit released this week found 47 per cent of the 565 fast-food outlets spot-checked nationally were not paying their workers correctly.

Have you been underpaid at work in Canberra? Email matthew.raggatt@fairfaxmedia.com.au