"What are they going to do if they are wrong?" Mr Joyce put it to Fairfax Media.
The Turnbull government has promised that power prices will fall under the NEG based on modelling of future scenarios.
Mr Frydenberg is understood to have assured Mr Joyce that he is doing everything possible as recommended by the Australian Competition and Consumer Commission, but Mr Joyce was not satisfied.
"I've lost all faith in modelling because the history with it has been so drastically wrong. There has to be [a] 'plan B' if prices don't go down, because if they don't go down they're going up, and if they go up, we go out," Mr Joyce said.
Labor premiers holding out against agreeing to the policy are demanding Prime Minister Malcolm Turnbull prove he has the support of his partyroom, which has been divided over a way to bring down carbon emissions since 2009 when Mr Turnbull lost the Liberal leadership to Tony Abbott over the issue. The Coalition currently has a majority of one seat.
The National Energy Board, which wrote the National Energy Guarantee, is predicting households could save up to $550, of which $150 is directly attributed to the policy which would force the energy sector to guarantee reliability of power and meet Australia's commitment to reduce its emissions by at least 26 per cent by 2030.
Mr Joyce joined other prominent critics, including former prime minister Tony Abbott, in rubbishing the calculations.
Liberal backbencher Craig Kelly, who argues Australia cannot affect the globe's temperature, told Fairfax Media it would be no bad thing if the government's policy were unable to pass the Parliament before the election, expected early to mid next year, as it would give the government a chance to rewrite its policy and reset its focus.
"What is beneficial to the Coalition is that voters understand we want to give prices priority over emissions," he said.
"I don’t think that legislation could be presented on nine o’clock on Monday and be expected to be voted on at 9.45am."
Queensland backbencher George Christensen is another government MP who has raised concerns about the NEG.
"I will be looking very carefully at how [it] will affect potential investment in new affordable baseload power and power prices in general," he said.
Mr Frydenberg said there was strong support for the NEG in the Coalition party room, telling Insiders on Sunday: “My colleagues have been briefed by the miners, the manufacturers, the farmers, the industry groups who say this is the only game in town to reduce people’s power bills.”
He said the Victorian Labor government, which on Friday left the policy's future in doubt, had been "spooked" after lobbying by inner-city Greens voters.
“We have to disassociate the crass, short-term political calculations going on in Victoria from the long-term national interest."
Federal Labor wants a 45 per cent emissions reduction target, rather than the 26 per cent target the government says would be reviewed in 2024.
Shadow energy minister Mark Butler said Labor would not support "an investment setting that will see not a single new energy project built in this country for an entire decade".
"Malcolm Turnbull’s investment framework will see no investment in renewable energy over the course of the 2020s," Mt Butler told reporters in Adelaide on Saturday.
"We know that the surest way to bring down power prices is to expand renewable energy."
With Dana McCauley