Australia’s environment laws have been “white-anted with loopholes” and non-compliance takes place on a “scandalously huge scale”, a Senate inquiry into threatened species has heard.

The inquiry into the rate of faunal extinctions was established after a Guardian Australia investigation found that Australia’s 1,800 threatened plants, animals and ecological communities were poorly monitored and conservation efforts inadequately funded.

At a hearing in Canberra on Monday, Martin Taylor, the protected areas and conservation science manager from WWF, said 7.5m hectares of threatened species habitat had been destroyed since the Environment Protection and Biodiversity Conservation Act 1999 came into force. In 90% of cases there was no evidence that the clearing had been referred for assessment under the act.

“We’re looking at a national scandal here to have such massive and pervasive non-compliance with federal legislation with no corresponding evidence of any enforcement action,” Taylor said.

He said lack of transparency meant it was unclear what enforcement action had taken place.

“How much is the department, in essence, approving by failing to even discover what’s happening or by investigating it and then deciding not to prosecute, which has happened in case after case after case that we have looked at?” he said.

WWF and the Australian Conservation Foundation told the inquiry the position of the threatened species commissioner was vulnerable to government interference and should have independent powers to enforce biodiversity laws.

ACF policy analyst James Trezise said both the current threatened species commissioner, Sally Box, and her predecessor, Gregory Andrews, had been successful in raising the public profile of threatened species.

But he said the position was “not an independent voice for conservation” because it sat within the federal Department of Environment and Energy.

“The commissioner... is not a commissioner, in the sense that a commissioner is normally someone who is defined at law and independent from government,” he said. “We would be more comfortable with that being called a threatened species ambassador.”

Asked by the committee chairwoman, Greens senator Janet Rice, if ACF would like the role to continue, he said: “If it were to continue we would like to see it be an independent statutory authority for threatened species, rather than a Twitter machine.”

The ACF and WWF are part of the Places You Love alliance, which has proposed an independent body similar to the Environmental Protection Authority in the United States.

That would allow environmental decisions to be challenged by third parties; Australian law allows for challenges only on administrative grounds. Provided you ticked off the procedural requirements, Trezise said, you could allow a species to become extinct.

Box, who gave evidence alongside her department colleagues, said that ensuring community engagement and negotiating partnerships around threatened species conservation was a key part of her role.

She said the 20 priority species in the threatened species strategy — which has been criticised for not including any reptiles, fish or invertebrates — delivered “umbrella” conservation efforts, such as feral cat eradication, which helped a variety of other threatened species that lived alongside target species.

The department said it had “very limited jurisdiction” in policing activities such as land clearing, which came under the purview of state and territory governments, and said it preferred mediation to prosecution when laws were breached.

Deputy secretary Dean Knudson said some areas of land clearing in Queensland had been referred for federal assessment and that rates of land clearing had fallen.

“When we take a look at land clearing in the entire country, the rates of land clearing have actually declined and indeed we are seeing more regrowth than we are clearing,” he said.

Last week, new data showed forests covering 770,000 hectares had been bulldozed over the past five years in the Great Barrier Reef catchment area alone.