The agriculture industry has been a long critic of the national environmental legislation, which often clashed with state regulations and required farmers to make an ecological judgement without specialist training or knowledge.

The Australian Conservation Foundation report found more than 420,000 hectares of land where "threatened species are likely to occur" was cleared in Queensland in 2018/19 without federal oversight.

Under the Environmental Protection Biodiversity Conservation (EPBC) Act, any land clearing that could impact a threatened species should be referred to the federal government. But the agriculture industry is critical of the legislation, which requires the landholder to judge if the clearing requires federal scrutiny.

AFC national nature campaigner Jess Abrahams said the report identified thousands of possible breaches that should have been investigated by the Department of Climate Change, Energy, the Environment and Water, however there was no record of any enforcement action.

Mr Abrahams said while other land clearing intensive industries, such as mining and property development, regularly referred their activities to the EPBC, compared to only 4 per cent of the reviewed agricultural land clearing.

He pointed to one example of an open cut coal mine in the Bowen Basin that referred potential clearing activity to the federal government. The application was withdrawn in 2015 and within a year more than 250ha of the environment referred to by the mine was cleared for agriculture without any federal oversight.

"A double standard in the enforcement of national environment laws is allowing hundreds of thousands of hectares of habitat for threatened species to be bulldozed without penalty or consequence," Mr Abrahams said.

"While mining companies and property developers sought and received approval to clear 25,000 hectares of habitat in the last decade, this research shows in a single year pastoralists destroyed three times that amount in Queensland alone without even seeking approval."

AFC called on the government to use its data to investigate the "unauthorised habitat destruction" and tighten land clearing laws in the upcoming reform of the EPBC Act.

AgForce chief executive Michael Guerin said farmers wanted to do the right thing and were forced to wade through an ocean of poorly-designed legislation. He wants a single system to assess land clearing applications against the criteria of all levels of government.

"We have three layers of government with gaps, overlaps and no clear pathway and it produces perverse outcomes for biodiversity," Mr Guerin said.

"Whether the answer [to the application] is yes or no, that's not the issue. The issue is there is no clear pathway."

IN OTHER NEWS:

Mr Guerin rejected the notion his state had an issue with agricultural deforestation as a "blatant lie that is causing a lot of hurt".

"It's a straight out lie, that sort of nonsense needs to stop," he said.

Environment Minister Tanya Plibersek was asked several questions about agricultural land clearing under the EPBC Act, but she referred questions to her department, who did not respond to specific questions.

Labor will respond to the Samuel Review in December, which will outline the government's reform agenda for the EPBC Act, including concerns around the cumulative impacts of regulated and unregulated land use.