Industry leaders are calling for shooting licences to remain readily accessible for farmers, arguing that they are vital in the battle to prevent damage to crops and livestock.
The NFU says it is important farmers have access to effective general licences that are fit for purpose and simple to use.
Individual licences are not the answer and any new system must reflect the role farmers play in providing food for the nation, it said.
NFU director-general Terry Jones said the union recognised the need to be more open about the non-lethal pest control measures employed by farmers – something that could be incorporated into a new system requiring better record-keeping.
But he warned: “Without a means for farmers to control pest birds, there can be devastating impacts on both crops and livestock.
“We saw these impacts first hand earlier this year when the licences were abruptly revoked and farmers do not want to see a repeat situation in the future.”
The NFU made the comments in response to a Defra consultation on the long-term future of general licences.
The consultation was launched by the government earlier this year following a legal challenge by wildlife campaign group Wild Justice.
Wild Justice campaigner Mark Avery said jay, magpie, rook and jackdaw should be removed from the general licences for the purposes of protecting fauna and flora.
Lethal control of carrion crow should only be permitted in more limited circumstances, he said.
Caroline Bedell, of the British Association for Shooting and Conservation, called for existing licences to be extended for 12 months.
This would allow the consultation findings to be adequately considered and avoid any sudden changes, she said.
“A fit-for-purpose licensing system will see the whole process easy to understand and light-touch,” said Ms Bedell.
“The decisions taken by Defra must be rooted in science, and where that is missing, practical experience.
“Enough time and resources have been spent on unnecessary meddling within the licensing system.
“Now is the time for Defra to be progressive in its outlook and secure for the future this essential tool for controlling wild birds.”