There are calls for an inquiry into the connections between the farming industry, the National party and decisions by the New South Wales Office of Environment and Heritage over allegations the agency dropped a land-clearing investigation after intervention from a Nationals MP.

The NSW government is expected to pass legislation within days making the clearing of native vegetation easier, by allowing farmers to do so without approval in many cases.

ABC’s Lateline reported on Monday night that the NSW Office of Environment and Heritage had dropped an investigation into alleged illegal land-clearing by 12 farmers in the Wee Waa area in western NSW.

The investigation was suspended in May 2015 after an email from NSW Nationals MP Kevin Humphries, seen by Guardian Australia, saying that inspections of the land would be the “start of something that will escalate very quickly between farmers from around the state and the authorities”.

He said: “I strongly urge that agencies do not seek to engage landholders on this particular issue at this time – it is too explosive and not warranted.”

The email came less than a year after the 2014 murder of NSW Office of Environment and Heritage worker Glen Turner. He was killed by farmer Ian Turnbull during a site inspection, as part of an ongoing investigation into allegations of illegal land clearing.

In internal OEH correspondence, Humphries email was interpreted as a threat, and the risk of “catastrophic” consequences associated with an inspection was thought to be “extreme”.

In one email an environment officer said: “I am of the opinion that the comments of Mr Humphries amount to a threat which cannot be adequately assessed in the available time.”

“This latest information makes the situation less tenable and would now require a police presence which would not be forthcoming given the short time frame,” he said.

The OEH told Guardian Australia it had decided to postpone site inspections in the Wee Waa area for operational reasons.

“OEH received an email from Mr Humphries,” its spokesman said. “This had no impact on the decision to postpone the investigation. The decision to postpone the investigation was made for operational reasons.”

The office said it received an average of 423 native vegetation clearing reports a year and focused on the most serious.

“For the period of time 1 July 2011 to 30 June 2016 OEH compliance activity has resulted in 520 advisory letters, 320 warning letters, 78 penalty notices, 42 remedial directions, 14 native vegetation prosecutions and secured penalties exceeding $1m.”

On Lateline Humphries denied he had perverted the course of justice.

Sue Higginson, the principal solicitor at the NSW Environmental Defender’s Office, said the intervention by Humphries raised serious concerns about the integrity of environmental protection laws in NSW.

“Where you are talking about the integrity of laws, it’s important that there’s a transparent process,” she told Guardian Australia. “What is concerning here is there appears to be a behind-the-scenes intervention.”

The chief executive of the Nature Conservation Council, Kate Smolski, called for a full investigation into the connections between big agribusiness, the National party and decisions by the OEH to drop investigation.

“The intervention of Nationals MP Kevin Humphries appears to have been an attempt to shut down legitimate investigations into land clearing,” she said.

Kevin Evans, the chief executive of the National Parks Association said: “The disturbing revelations last night showed a politically well-connected class of landholder apparently operating above the laws that apply to the little guy.”

He called for the changes to NSW laws to be halted until the alleged political interference by Nationals MPs in the enforcement of existing laws was fully investigated.

The changes to NSW land clearing laws, expected to pass parliament this week, are widely believed to allow a significant increase in broadscale clearing.

One of four scientific advisers on the government’s changes, University of Queensland biologist Hugh Possingham, resigned from the government’s independent biodiversity legislation review panel in protest, saying its advice was being ignored.

He warned that broadscale clearing could double in NSW as a result of the changes.

Farmers will be allowed to clear native vegetation without approval in many cases and others will have access to “offsets”.

In Possingham’s resignation letter he said that despite the government agreeing to adopt and implement all the recommendations of his panel, it did not do so.

“A key intent of the report is that broadscale land-clearing would only be possible through the biodiversity offsetting process,” he said. “Biodiversity offsetting, by definition, means no net decrease in the quality and quantity of native vegetation.”

Possingham said despite that, the proposed legislation contained “a series of “codes”, such as ‘the equity code’, that will enable broad-scale clearing of hundreds of hectares of native vegetation on individual farms without offsetting”.

The changes include the scrapping of three laws: the Native Vegetation Act, the Threatened Species Conservation Act and the Nature Conservation Trust Act. Parts of the National Parks and Wildlife Act will also be repealed. The legislation will be replaced with two new acts: the Amended Local Land Services Act and the new Biodiversity Conservation Act.

As a result of the changes, as well as plans to continue allowing logging of native forests, a recent report by the National Parks Association said endangered koala populations in NSW were “under siege”.

“The NSW government is completely failing to conserve and protect koala habitat,” the report said. “Koalas can lay claim to be the most poorly managed species in eastern Australia at present – which is hugely disappointing in light of their beloved status.”

Humphries has been contacted for comment.