The Liberal Democrat leader called on firms to "come clean" about the extent to which customers bills were affected.
His comments come just days after some of the "Big Six" energy firms were accused of overcharging customers by billions of pounds.
In response many of them banded together to urge ministers to scrap the levies, pledging an instant cut in bills in return.
Prime Minister David Cameron has said that he wants to "roll back" the environmental taxes. But Mr Clegg has said he will resist any changes that hit poorer households.
Last night a Conservative minister played down Mr Clegg's suggestion that the green levies could be removed from bills and added to general taxation.
Earlier Mr Clegg said that it was "totally implausible" that the up to 10% increase in consumers' bills seen in recent weeks was triggered by green levies.
He called on firms to "come clean" about how they were passing on the costs to customers.
"I would say to the Big Six that it's time that they opened their books, it's time that they were straight with people," he said.
Earlier Mr Cameron had announced that a planned inquiry into the market would begin immediately.
The Department of Energy and Climate Change also released data suggesting that homeowners could save an average of £131 if they banded together to switch suppliers.
But consumer groups say that such is trust in energy companies that customers are reluctant to change.
Mr Clegg reiterated his advice that those wanting to switch wait until the "big six" have finished the latest round of price increases.
Mr Fallon told MPs on the Commons Environmental Audit Committee that green levies accounted for 9% of average dual-fuel bills.
Of that around 5% went to energy efficiency and the other 4% to support low carbon energy sources.