Three businesses across the Belconnen area had more than $5000 worth of "questionable" transactions during a trial of the ChooseCBR voucher scheme last December.
ACT Business Minister Tara Cheyne made the revelation in the territory's parliament on Tuesday.
"One pattern of questionable transactions was identified across three merchants," Ms Cheyne said.
"The merchants were provided an opportunity to explain their transaction patterns and were not able to do so satisfactorily.
"The merchants were removed from the program before the full rollout."
When first asked what the nature of the questionable transactions was, Ms Cheyne said she did not have that detail.
However, later in the day Ms Cheyne revealed during question time that there were three businesses across the Belconnen region that had claimed $5355 of vouchers that were questionable.
The total value redeemed across the three businesses was $6156.
Ms Cheyne said the government was unable to recover this funding.
"The cost of recovering the money outweighed the actual amount of money in question," she said.
The controversial discount voucher scheme dominated sitting day at the ACT Legislative Assembly on Tuesday.
It started with a 32-page ministerial statement from the Business Minister who sought to strongly defend the scheme.
Ms Cheyne was then grilled by the opposition in question time about the scheme, followed by a motion that called for the government to write a letter to the auditor-general asking for the scheme to be audited.
The motion put forward by opposition business spokeswoman Leanne Castley was heavily amended by Ms Cheyne.
It was amended to say that the government would commission an independent and comprehensive review of the program.
The amended motion also said that Ms Cheyne had written to the auditor-general to advise that an independent review would be undertaken and that this would be shared with the auditor-general.
Ms Cheyne said the findings would also be publicly released.
"The government will analyse the spread of activity across businesses and consumers," she said.
"The review will also evaluate its stimulus impact to determine if something similar would be appropriate in the event of a further economic downturn."
Ms Castley slammed the amendments.
"I truly believe that the Canberra business community deserves a comprehensive audit," she said.
The $2 million scheme provided ACT government subsidised discounts of up to 50 per cent for people to use at participating Canberra businesses.
The scheme, which followed a December trial, started on June 9, however, it was plagued with technical difficulties due to demand that caused the site to crash. The ACT government was then forced to pull the site for a week to fix those issues.
But while Ms Cheyne said there was no indication of misuse she could not rule out the fact that some people may have used multiple email accounts and phone numbers to take advantage of multiple vouchers.
"It may have been possible that a person may have registered with more than one email account if they had access to more than one mobile phone. We have no way of verifying this," she said.
"Given the value of the program, and the effort an individual would have to go to, this was a risk that was considered to be low.
"It would be disappointing if what has been alleged was true as this is absolutely not within the spirit of the program."
Each person was eligible to use three vouchers a day. Customers were able to get $10 off when at least $20 was spent, $20 off when at least $40 was spent and $50 off when at least $100 was spent.
To sign-up to the scheme users were required to use a unique email address and phone number.
The government has also faced criticism around the fact it has not released the names of businesses that had the most vouchers claimed.
The government firstly attributed this to privacy reasons but when asked what privacy legislation prevented this, the government deferred to "commercial-in-confidence".
However, Ms Cheyne said the government was seeking legal advice around the release of names.
"This is transaction details for businesses and that might potentially include or suggest some sensitive information for businesses," she said.
"I'm not sure that businesses though if they were a successful business under this scheme that their names would be released.
"That's why we are just wanting to make sure that we get that legal advice before making any further decisions about what we release there."
In her speech to the Legislative Assembly on Tuesday morning, Ms Cheyne also took aim at the media for focusing on Chemist Warehouse Belconnen's participation in the program.
"There was plenty of commentary in the media and, in turn, social media, about particular businesses - and one which received more coverage than any other - appearing to get 'more than it's fair share'," she said.
"The reporting was unfortunate in giving that impression; in that it attempted to delegitimise these businesses' reasons for participating in the scheme; and it took attention away from the hundreds of businesses participating in the scheme.
"It also undermines that fact that franchisees are small businesses; owned by locals who employ locals."
There were long queues at the store on Friday morning with people lining up to take advantage of the vouchers.
The Canberra Times received several reports from members of the public who had questioned the lines before a photographer took images of the lines outside the store.
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