The Sustainability Council says Government ministers are trying to play down a big deficit in the carbon accounts by changing the way the information is publicly disclosed.
Emissions Trading units are traded within the scheme, but the Government gives some to polluters who can't pass on their emissions costs to consumers.
Those units show up as a cost to the Government.
Sustainability Council executive director Simon Terry said that by the end of this year the Government will have a carbon liability of $1.3 billion.
He said documents he has obtained show that ministers have asked officials to consider whether the units should still be valued in the Crown's financial statements.
Climate Change Minister Tim Groser declined to comment because he has not been fully briefed on the documents.