It is one of the more neglected dimensions of the badger cull, but one that could reignite the controversy surrounding the attempt to control the spread of bovine tuberculosis.

Conservationists have long claimed that eliminating badgers from certain areas is likely to trigger an increase in other predators, such as foxes, leading to serious consequences for species and habitats. But the government has refused to publish data showing what impact the cull is having on local ecosystems for fear that the results will be used by animal rights activists to identify the farmers and landowners carrying out the extermination.

Now, following a three-year battle, the Information Commissioner’s Office has told Natural England – the government’s adviser on the natural environment – to provide the analysis within weeks or risk ending up in the high court. The ruling will also have significant consequences for the other information that the body is withholding on the grounds of public safety, conservationists predict.

A recent report for the Welsh assembly suggested that removing badgers would see numbers of other predators – such as foxes, stoats and weasels – increase, something that could have a negative impact on ground-nesting birds, notably the chough, a member of the crow family. Research sponsored by the Department for Environment, Food and Rural Affairs and published in 2007 suggested that “badger culling … is likely to result in markedly higher fox densities. This raises issues relating to the costs of predation on livestock and game, the ecological impact of foxes in conservation terms as predators of ground-nesting birds and hares, and risks to public health as potential vectors of rabies”.

In 2011, ahead of pilot culls in Gloucestershire and Somerset, the government’s then Food and Environment Research Agency acknowledged that “removing or reintroducing a dominant predator in any ecosystem may have a widespread impact upon a wildlife community, and that the impact is hard to predict”.

It called on the government to conduct proper analysis, but Natural England has until now refused to release the analysis, telling the information commissioner that disclosure “of the withheld information will lead to a materially increased risk of landowners … being victims of intimidation, harassment and criminal damage”. The commissioner has now decided that these fears are insufficient grounds for withholding the information.

“This opens the floodgates to a whole range of issues, not just about the cull’s impact on other predators, but other information it is withholding relating to cost, scientific validity and monitoring,” said Dominic Dyer, chief executive of the Badger Trust. “Tens of thousands of badgers are being targeted across the country in a blind cull where no badgers are being tested for TB and where we have very little information on the ecological impact of their removal.”

The ruling could be embarrassing for the new Defra secretary, Michael Gove. A failure to have conducted the analysis will trigger a torrent of criticism from both sides. Since the badger cull started six years ago, it has been expanded to Dorset, Devon, Cornwall, Herefordshire and Wiltshire and is likely to be introduced in Cheshire and Derbyshire later this year. Last year almost 11,000 badgers were killed as part of the cull.

The National Farmers Union believes the cull, which needs to kill 70% of the badger population in the targeted areas to be effective, is key to controlling and eradicating bovine TB, the spread of which led to the slaughter of more than 29,000 cattle in England in 2016, with around 250,000 killed since January 2008. Farmers say the disease has cost the taxpayer £500m in England in the past decade and that this will rise to £1bn over the next 10 years.

But Dyer said that the government was sitting on key data that suggested the cull was not working: “If you look at the cull zones and the surrounding areas there is no evidence killing badgers is reducing TB.”

A failure to have conducted an impact assessment would be a breach of the Bern convention on the Conservation of European Wildlife and Natural Habitats. As a result, the UK government could see itself dragged through the courts.

Dyer added: “If we find that the government has not done a proper ecological assessment on removing the badgers, it could lead to a challenge under the convention.”

A spokeswoman for Natural England said: “We are considering the [information commissioner’s] decision.”

The ruling comes amid claims the UK’s badger population of half a million is under threat. An estimated 50,000 badgers are being killed on the roads each year and as many as 30,000 more could be culled by October.