They are the children's book naughty-but-cuddly heroes, pinching from the big bad farmer to feed their growing brood.

Depending on your point of view, the humble rabbit is a cute sight in the countryside or a pest that breeds like, well, rabbits, destroying crops and costing hard-working farmers money.

But now the Government, in the form of an obscure change to an equally obscure agricultural rule, appears to have come down on the side of rabbits, and struck what is being described as yet another blow to the honest farmer.

Laws written 60 years ago gave farmers the power to ask the Government to intervene if their neighbouring landowner was allowing a rabbit infestation to get out of hand, causing damage to their crops on the other side of the hedge. The ministry would issue an edict ordering the farmer to cull the rabbits, or face a lump sum fine and then a daily fine for each day there was still no action.

But now Natural England, the latest quango to rule over such matters, has announced the enforcement rules would be scrapped, and that they would only intervene in "exceptional circumstances" where there was a "national problem".

This change has been held by the countryside lobby as another example of a Government that cares little about farmers – the Country Land and Business Association (CLA), the National Farmers' Union and the Countryside Alliance all lined up to attack the Natural England switch.

CLA president Henry Aubrey-Fletcher said: "When the whole world is worrying about whether there is sufficient food to feed us, the decision seems irresponsible. Rabbits cause tremendous damage to crops and they need to be controlled."

NFU lawyer Julie Robinson said: "What concerns me is that this is Natural England pulling back from its statutory duty because it does not feel that any order to compel people to kill rabbits fits in with their overall brief, which is the protection and enhancement of wildlife, rabbits or otherwise."

Tim Bonner labelled the row "Rabbitgate", and reassured members of the Countryside Alliance his organisation would be lobbying ministers over the change. "The rural community increasingly sees Natural England and Defra as being infested with a bunny-hugging mentality which is far removed from the realities of rural life," he said.

"When it continues to act in such a ludicrous way without consultation or logic, then the Government can't escape criticism that it has no understanding of rural issues."

But Natural England hit back, saying they were stepping out of their enforcement role on the issue because it was so little used.

In the past three years, it emerged, only 60 requests for action were made by farmers about their neighbours to the Government, and of those only three ended up with action being taken.

The countryside lobby's attempts to find a farmer who would now be powerless in the face of a rabbit invasion from next door is proving difficult.

Natural England said farmers should settle their disputes between themselves, using the courts if necessary. The laws requiring the Government to act as rabbit police were created in the pre-myxomatosis days when the rabbit population was far larger than today.

They also point out that the top fine facing a farmer determined not to sort out a rabbit problem damaging his neighbour's crops was a "relatively modest" £500. A Natural England spokesman said: "We believe that the long-term resolution of disputes over rabbits between neighbours is best achieved by co-operation.

"Without co-operation, problems are almost certain to recur.

"If co-operation fails, occupiers do have options such as rabbit fencing to prevent damage. It is understandable that those suffering damage through the inactivity of neighbours feel that they should not pay to resolve the problem.

"However, given that compulsion is often not the most effective way of resolving problems with rabbits, Natural England feels it would only be appropriate to spend public money issuing and enforcing notices in exceptional circumstances. These would, for example, be a situation that had national rather than local significance; it would not normally be damage at a holding or even parish scale."

But one Wiltshire arable farmer, who declined to be named, said Natural England had got it wrong. "Most farmers get on with our neighbours and sort something like this out with no fuss or bother," he said.

"But if there is someone who doesn't do enough to sort it, you can always use the threat of calling in the ministry and I've never heard it not do the trick.

"The prospect of getting people from Defra or Natural England or wherever, crawling all over your farm is enough to make the most stubborn farmer do something quick. That's why so few of these orders are ever actually requested and even fewer ever made, and that's why Natural England doesn't think it's a problem.

"What will happen now though, I don't know."