The killing of thousands of “pest” birds each year including crows, rooks, jackdaws, magpies and woodpigeons is to be challenged in court by wildlife campaigners including Chris Packham.

Wild Justice, a group newly created by Packham and fellow conservationists Mark Avery and Ruth Tingay, is launching legal action against Natural England, the government’s conservation watchdog, for issuing a general licence that allows the unlimited slaughter of certain wild birds all year round.

Species including jays, lesser black-backed gulls, Canada geese and non-native parakeets can be killed without a specific licence if they are causing damage to crops or forestry or pose health or safety risks to humans. Shooters or trappers do not have to explain why alternative non-lethal measures such as scaring are impractical, or report on how many birds are killed.

According to Wild Justice, this is unlawful under British wildlife laws as well as the EU birds directive.

“We’re not saying that no birds should ever be killed but the means that Natural England have chosen to authorise this is unlawful because they are not taking enough care to judge individual cases, or indeed any case at all,” said Avery.

“It appears to us that Natural England – the government’s wildlife regulator that should be a protector of wildlife and a defender of wildlife law – has been an unlawful killer of wildlife.”

Most wild bird species are protected unless someone obtains a specific licence from NE to allow their killing. The Guardian recently revealed that NE issued licences to destroy 170,000 wild birds, eggs and nests, including rapidly declining species such as curlews and swifts, in the past five years.

But these figures are dwarfed by the number of unprotected crows, gulls and other wild birds that are killed under NE’s general licence, which it issues at the start of each year.

Wild Justice is seeking a judicial review, launching crowdfunding to raise £36,000 to cover the cost of the legal action.

If the courts find the general licence is unlawful, NE could be forced to issue thousands of specific licences to allow the killing of magpies and other species, vastly increasing its workload.

The conservation watchdog’s budget has been cut by more than a half in the past decade, although this week’s appointment of Tony Juniper as its new chair has raised conservationists’ hopes that the watchdog will be revitalised.

NE’s director of operations, James Diamond, has said: “All wild birds are protected by law. However, for almost 40 years licences have been issued for bird control under the Wildlife and Countryside Act 1981 in certain circumstances, such as to protect the public.

“This could be where a bird is trapped in food preparation premises or is posing a threat of bird-strike at an airport.

“These licence applications are carefully considered by our experts – including our ornithologists where necessary – and are only granted when all other measures have been explored.

“The number of birds that may be killed is strictly limited and won’t harm the conservation status of any species.”

Marian Spain, the watchdog’s interim chief executive, said: “Natural England has noted and responded to a pre-action letter from Wild Justice. Natural England will be carrying out a review of general licences as planned. In the meantime all existing licences remain in operation.

“We take our approach to licensing seriously, taking into account the needs of wildlife and the needs of people. We strive to make these licences as effective as possible, considering both the evidence base relied on and the administrative burdens that they impose.”