The federal government insists the GST does not apply to its carbon tax, warning action would be taken against businesses that claimed otherwise.
However, air-conditioning firms, data contractors and waste firms have begun applying the GST on top of the carbon tax.
NSW electricity companies also confirmed the 10 per cent GST would be applied to power bills after the carbon tax had been added.
The government says laws have been specifically amended to ensure that no GST is payable on the $23-a-tonne carbon tax applied to about 300 of the nation's largest carbon emitters.
"The carbon price does not change how the GST operates," Climate Change Minister Greg Combet and Assistant Treasurer David Bradbury said in a joint statement on Friday.
"The GST does not apply to the carbon price, it applies to the supply of goods and services," they said.
The government also has referred one of the nation's largest waste disposal firms, J.J. Richards, to the Australian Competition and Consumer Commission.
The firm has told its customers the carbon tax will cost $25.30-a-tonne "including GST".
"This is wrong," the ministers said.
"Any business jacking up their prices and falsely blaming the carbon price could be liable for fines of up to $1.1 million."
However, cabinet secretary Mark Dreyfus told journalists in an earlier interview: "I don't think there's any doubt" that GST revenues will increase as a result of the carbon tax.
Shadow Treeasurer Joe Hockey said the "taxes on taxes" scenario revisited the pre-GST era of hidden wholesale sales taxes and would make the economy inefficient.
"The only area where you still have taxes on taxes is insurance which is the most hideous area of tax," Hockey told the Seven Network.
