The CSIRO says the Australian Petroleum Production and Exploration Association has misrepresented its research on coal seam gas.
In a statement yesterday the CSIRO said it had asked the APPEA not to air a CSG advertisement because it wrongly attributed quotes to the research body.
The advertisement claims CSIRO and government studies have shown "groundwater is safe with CSG," but the CSIRO refutes the claim.
"At no time has CSIRO made such a statement, and nor do the results of CSIRO research support such a statement," it said.
"CSIRO has stated on the public record that coal seam gas extraction is likely to pose a ‘low risk’ to groundwater quality through contamination."
"CSIRO has also indicated that groundwater levels will fall as a consequence of coal seam gas extraction."
"In some places this could see aquifer levels subside by tens of metres for tens of years; in others it is likely to reduce aquifer levels by several metres for several hundred years."
On Twitter APPEA chief operating officer Rick Wilkinson said the advertisements had been approved by Free TV Australia's Commercial Advice and the gas lobby had "taken CSIRO's comments on board".
Earlier this year CSIRO ecosystem sciences deputy chief Peter Stone said there was minimal risk of water or land contamination due to the CSG industry.