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Ministers and farmers argue the badger culls are necessary to tackle TB in livestock that can pick up the disease from wild badgers.
But activists insist it has little effect - and are furious the cull is being extended.
The two four-year pilot culls in Somerset and Gloucestershire should be completed using the "tried and tested" method of trapping the badgers in cages and then shooting them, the BVA urged.
The culls were designed to run for four years and anecdotal evidence from both cull areas suggests they are already helping to reduce bTB incidence in cattle and farms are starting to go clear of the disease.
The culls have so far cost around PS4,000 per dead badger - a terrible waste of money.
But the culls have divided the public, with farmers and rural communities desperate to find a way to curb devastating bovine TB.
David Bowles, from the RSPCA, said: "At last the Government has acknowledged that the culls have failed to reach their target numbers and failed to do it in the allocated time.
The RSPCA said while the culls may Antoinette Sandbach AM not result in the total eradication of badgers in England as a whole, it was possible in certain areas within the cull zones the loss could be total.
No information was given on where shooting of badgers had begun, but licences have been given for two pilot culls in west Gloucestershire and west Somerset, with around 5,000 badgers set to be killed in a six-week period across the two areas.
The pilot culls aim to ensure badgers can be killed humanely by marksmen.
Led by rock star Brian May, the 2,000 animal welfare supporters wore cardboard badger masks and chanted "stop the cull" in protest at pilot culls in west Gloucestershire and west Somerset.
As a result, farmers could not be confident they could cull enough badgers this year and two pilot culls that were due to start imminently will now take place next summer.