“Pest” bird species such as crows, woodpigeons and jays can no longer be freely killed in England after the government’s conservation watchdog revoked the licence permitting it.

The move by Natural England came after a challenge to the legality of the “general licence” by a new environmental group, Wild Justice, created by conservationists Mark Avery, Ruth Tingay and Chris Packham.

Natural England now plans to introduce a legal system of licences to allow 16 species of birds, including rooks, magpies, Canada geese and non-native parakeets, to be controlled. In the meantime, anyone wanting to control these species must apply for an individual licence, as they are required to if seeking to kill other more protected bird species.

Wildlife campaigners have greeted the decision, which came on Tony Juniper’s first day as the new chair, with delight, but many farmers – and some conservationists – were dismayed.

“It’s not every day that three part-time conservationists overturn decades of unlawful bird-killing,” said Avery. “England’s statutory nature conservation organisation has been shown to be allowing people to break wildlife law for decades.”

Natural England’s interim chief executive, Marian Spain, said: “We recognise this change will cause disruption for some people, but we are working hard to ensure it is kept to a minimum.

“We will bring forward interim measures as quickly as possible as the first stage of our planned review of the licences. We want to make sure our licensing system is robust and proportionate, taking into account the needs of wildlife and people.”

Farmers and land managers said the timing of the revoking of the licence came at the worst time for protecting livestock such as lambs, crops – and some wildlife.

Guy Smith, deputy president of the National Farmers’ Union (NFU), said it had “significant concerns” about the abrupt withdrawal of these general licences.

“They are absolutely necessary at this time of year when crops are particularly vulnerable to pests. For example, a flock of pigeons could decimate a farmer’s field of crops,” he said. “It is incredibly disappointing that farmers and growers find themselves in this position, particularly at this time of year.”

The conservationist Mary Colwell said the revoking of the licences came just when crows preyed on the eggs of endangered ground-nesting birds such as lapwing and curlew.

She said: “The general licence needs reforming and tightening but Natural England’s timing is appalling. Curlews lay their eggs on average on 21 April. If they lose their eggs – and camera traps reveal the biggest predators are foxes followed by crows – they won’t lay again this year. There’s no doubt that if you stop people controlling crows at this time of year the crows will take more eggs.”

Avery said Wild Justice’s challenge had only sought to halt the general licence from next year, and said Natural England could have better timed its announcement so farmers and conservationists had more time to apply for individual licences.

He said he hoped Natural England would consult all parties to design a better licensing system. “If you were designing a new system of licensing you’d get everybody around the table to talk about what is needed and how it should be administered,” he added.

According to the NFU, Natural England will issue interim measures to allow for the temporary control of these 16 bird species from 29 April before its wider review.