The controversial badger cull taking place in Gloucestershire should be stopped immediately, says the lead scientist on the board of Natural England, the organisation charged with making the decision.

NE, the nation's official protector of nature, will rule Monday on whether the night-time badger shoots can be significantly extended, following the revelation that marksmen fell far short of their initial legal targets.

The intervention by David Macdonald, chair of NE's science advisory committee and one of the UK's most eminent wildlife biologists, is a heavy blow for the environment secretary, Owen Paterson, and the National Farmers' Union, who argue that killing badgers to curb tuberculosis in cattle is scientifically justified and necessary.

The badger cull is also being jeopardised by a legal threat launched on Saturday.

Macdonald, a professor at Oxford University, said: "My personal opinion as a biologist [is] not to continue the cull. One could not have significant comfort that the original proposals would deliver gains to farmers. Extending the cull would make the outcome even less predictable and even more unpromising."

A 10-year trial of badger culling found that killing too few badgers over too long a period of time caused TB infections to rise rather than fall, since fleeing badgers spread the disease further afield, an effect called perturbation.

The new pilot cull in Gloucestershire was licensed by NE to kill 70% of the badger population in a specified area of the county in no more than six weeks, but the shooting of free-running badgers managed just 30% in that time.

Backed by Paterson, the cullers have now applied to NE for an eight-week extension to the killing.

Macdonald said: "Perturbation has undoubtedly been caused in Gloucestershire already and an extension by six to eight weeks is likely to worsen the perturbation even more."

He noted that the original, decade-long, trial carried out culls over periods of eight to 11 days to minimise perturbation.

The extension ruling will be taken by NE executives, who have already given a three-week extension to the badger cull in Somerset, where a higher proportion of badgers – 59%– were killed in the initial six weeks.

A second significant intervention also came on Sunday from the former environment minister Huw Irranca-Davies, who appointed the NE's chair, Poul Christensen.

Irranca-Davies, now a shadow environment minister, has written to Christensen saying that granting the Gloucester cull extension would destroy the credibility of the wildlife watchdog.

He wrote: "The hard-won reputation of Natural England for sound impartial and evidence-based advice which can support but also challenge policy makers is on the line. NE has built its reputation on scientifically robust, evidence-based and impartial advice to government, and a willingness to challenge government policy which departs from your core aim to safeguard England's natural wealth for everyone."

"This is not an attack on Natural England but an attempt to help it do the right thing, in the face of unprecedented pressure from political leaders," Irranca-Davies told the Guardian.

He said he was seeking reassurances from NE on the protection of "the integrity of the advice which government ministers rely on from NE".

He said seeking an eight-week extension "departs from any pretence whatsoever at having any scientific underpinning".

A Conservative attempt to scrap NE this year was blocked by the Liberal Democrats, according to Nick Clegg who said in September of the environment: "[It is] one area where we've had to put our foot down more than any other. It's an endless battle; we've had to fight tooth and nail."

Macdonald said: "It is tremendously important that a body like NE exists to offer independent advice – it is a jewel in the crown of the protection of nature. It is vital that the institution, which works tirelessly and diligently, is not only treasured but strengthened."

A spokeswoman for the Department for Environment, Food and Rural Affairs said: "Natural England is the licensing authority and any decisions on whether to extend the licences will be made by them." NE declined to comment.

TB infections in cattle have risen in the last 10 years and in 2012 cost taxpayers £100m and led to the slaughter of 28,000 cattle.

Macdonald said: "This causes affected farmers extraordinary stress and blight. [But] economically, the culls are extremely punishing for the farming community, who bear the costs. Extending the cull would make this worse."