Accelerating rates of tree clearing in Queensland are wiping out any cuts to greenhouse gas emissions the federal government has made through its $2.55bn Direct Action fund, according to the latest data released by the Queensland government.

The results also point again to apparent holes in the federal government’s greenhouse gas accounting, as its official figures maintain that land clearing in Queensland is reducing, and that changes in land use across the whole country are cutting emissions rather than adding to them.

About 40% of the clearing in the state identified in the latest figures occurred in catchments that drain water into the Great Barrier Reef, which will increase pollution affecting the struggling coral, sparking further calls for the environment minister, Josh Frydenberg, to use his powers under federal law to stop some of the clearing.

On Thursday the Queensland government released figures showing 395,000 hectares of bush had been cleared in 2015-16, according to its statewide landcover and tree study (Slats). That was up a third compared with the previous year and almost 50% compared with two years earlier.

The state environment minister, Steven Miles, said the clearing in one year in Queensland alone caused 45m tonnes of greenhouse gas emissions.

The centrepiece of the federal government’s Direct Action policy on climate change is its $2.55bn Emissions Reduction Fund, under which it pays companies to pollute less.

In the last auction of the ERF, the government paid an average of $11.82 for each tonne of carbon abated, meaning the emissions from Queensland’s land clearing cancelled out more than half a billion dollars of abatement paid for by the taxpayer – a fifth of the total fund in one year.

“Deforestation has a major impact on climate change,” said Lyndon Schneiders, national director of the Wilderness Society. “Ending deforestation would be a fast, cheap and effective way to cut Australia’s greenhouse gas emissions.”

Meanwhile, the federal government’s national greenhouse gas inventory, which is the country’s official source of climate change accounting, continues to find that across the whole country, changes in land use – which includes land clearing – amount to a carbon sink rather than a source.

In the latest federal government figures, for the year to March 2017, changes in land use are counted as an abatement of 0.1% of Australia’s greenhouse gas emissions. The report on the figures says Queensland’s land sector emissions have been “reducing over time”.

Changes in the way the federal government measures greenhouse gas emissions have led to revisions of historical reports, with significant amounts of emissions disappearing. Explanations given for the revisions do not fully explain the reduced emissions.

The environment department said in a statement Queensland data was used to prepare the national figures and informed the national inventories.

“Each year, we update land clearing estimates based on latest satellite data. Where applicable, we also revise estimates to reflect improvements in remote sensing and estimation methods,” a spokesperson said.

The large amount of clearing occurring in the Great Barrier Reef catchments has led to renewed calls for Frydenberg to use his powers under the federal Environmental Protection and Biodiversity Conservation Act to stop some of the clearing.

Frydenberg has previously stated that clearing activities require approval under the act if they “have, will have or are likely to have a significant impact on a matter of national environmental significance under federal environment law”.

He told the ABC in July the government had powers to enforce those laws and would continue to do so.

But a WWF report from July found 99.2% of properties where land had been cleared that appeared to need approval under the act, had failed to gain it. The only time the federal government forced a property owner to gain approval, it led to fighting within the federal Coalition.

“The amount of clearing in reef catchments should be ringing alarm bells with minister Frydenberg,” said Martin Taylor, a conservation scientist at WWF-Australia.

“When the Queensland parliament rejected tougher laws the commonwealth was the last line of defence. Minister Frydenberg’s department has the power under the EPBC Act to rein this in. But the EPBC protections only work if they’re used and that’s not happening,” Taylor said.

Frydenberg’s office did not respond to questions about the matter.