Yesterday, Defra Secretary Owen Paterson informed MPs that, after six weeks of culling, the trial badger cull in Gloucestershire had failed to meet its target, killing 70 percent of the local badger population. The announcement that markspeople in Gloucestershire killed 708 badgers (30 percent of the estimated population) follows news that the Somerset cull company has been granted a three-week extension to culling after falling short of its target last week.

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The company running the Gloucestershire cull has reportedly requested that culling is extended to 14 weeks in the trial zone. Natural England is expected to grant an extension within the next few days. The Badger Trust reacted strongly to the news on Thursday. A Trust spokesperson said, "This is yet another contemptuous and wilful swipe against science following an extension and gerrymandering with badger populations in Somerset."

Meanwhile, the latest controversy to arise from a policy marked by its secrecy and divisiveness is speculation over the cause of repeated reductions to Defra's population estimates. Fresh estimates made just before the two trial culls started (reducing the estimated number of badgers by around 1,000 in each cull zone between Summer 2012 and this year) followed the postponement of culling in October 2012 due to uncertainty over numbers. Since that time, official population estimates within the cull zones have changed three times in the past twelve months.

Defra officials maintain that the latest slashes to population estimates are the result of a cold winter which brought severe flooding to parts of the South-West, disease and a lack of food. However, badger experts have accused ministers of failing to support their assertions and wilfully ignoring two major issues.

On Thursday, a number of badger experts told the Guardian's environment writer Damian Carrington that tampering with hair traps used to count badger numbers by protestors and illegal culling (evidence of which has been uncovered most recently by Sky News) must play at least some part in the dramatic fluctuations in badger numbers seen at the two trial cull areas. Closely monitored badger populations elsewhere have remained constant for the past five years, according to workers at sites in nearby Gloucestershire and Oxfordshire.  

Defra reporting on badger populations at Woodchester Park in Gloucestershire has been ongoing for 25 years, although the latest data is incomplete and has not been made public, records show that the badger population has not fluctuated so widely in all the years of reporting as it has in the two cull zones.

Reports from police officers working on wildlife crime and BBC investigators over the past two years suggest persecution is a problem with deep roots. Environment Secretary Owen Paterson has been loath to condemn illegal killing explicitly. Last week, when presented with evidence of 14 illegal DIY gassing 'trials' being organised by farmers in the South-West, Mr Paterson said "that's unfortunate." Gassing of wildlife has been illegal in Britain since 1982 and, as the Environment Secretary pointed out and the influential RBCT trials established several years ago, such reactive culling can lead to overall increases in bovine TB.

The Defra Secretary told MPs last week that figures from Woodchester Park are not yet available, but that badger populations had dropped off in 'other areas'. Carrington has since established that these 'other areas' are in fact the cull zones.

In light of mounting evidence, including analysis from Rosie Woodroffe, a badger expert at the London Zoological Society who participated in the previous government's ten-year Randomised Badger Culling Trials, and said this week that either illegal persecution or interference from protesters would be more likely to result in the shifting figures observed in the cull zones than natural factors, Defra has not altered its official line.

A spokesperson repeated on Friday, "We have no evidence of any illegal culling activity. If anyone suspects that illegal culling is taking place they should present the evidence to the police."

Despite Defra's reluctance to comment further on the possible reasons for decline, or even state whether the department is looking into their potential causes, pressure on the government to provide answers is increasing by the day.

On Friday, Dominic Dyer, Policy Advisor for wildlife charity Care for the Wild, told Farming Online, "The government says that natural fluctuations would account for [the drop in badger unmbers], but that is being dismissed roundly by experts. There is obviously potential that the numbers were wrong in the first place, either by error or by interference from protestors. But from 4,500 to 1,500 in just the Somerset zone within a few months? There has to be more to it than miscounting."

Suggesting that Defra's tactics and conduct have given the impression that there is a 'green light' to kill badgers, Mr Dyer added, "A report last week revealing that at least 14 farms in the Somerset area were involved in illegal gassing opens up the very real possibility that badgers are being taken out illegally under the radar of the legal cull. With uncertainty about the number of badgers out there, we could be stumbling into local extinctions. That might satisfy some farmers, but it'll be a sad and barbaric day for the rest of the country."