The Essential Services Commission on Tuesday said it took the action against the accredited businesses that took part in the Victorian Energy Upgrades program.
The scheme was created to replace ageing and energy-inefficient appliances, with installers allocated carbon credits to then on-sell to energy retailers to offset their emissions.
But it was suspended in June amid reports that large numbers of fridges were being dumped on the street or given to customers who did not want them.
The commission found the nine businesses failed to comply with the scheme's compulsory installation, evidentiary and record-keeping requirements.
It suspended the accreditation of one business, while a second business now has accreditation conditions.
Both businesses have been banned from carrying out fridge activities under the scheme.
Another seven businesses have received formal warnings.
The commission first started looking into the breaches in June when it paused registering energy-efficiency certificates under the scheme.
"The investigation found evidence of repeated non-compliance by a small group of businesses," commissioner Sitesh Bhojani said.
"Two accredited businesses in particular demonstrated a clear disregard for these important program rules."
As part of its enforcement action, the commission rejected the registration of 18,238 energy-efficiency certificates created by the businesses for 85 separate fridge activities.
Some 2.8 million certificates have been created for fridge activity under the government program.
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