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A Labour motion calling for an imminent cull of badgers in England to be abandoned was defeated in the House of Commons on Wednesday by 49 votes. Government whips ensured a victory for ministers after a previous vote, prompted by a public petition, had seen MPs vote against the cull.

The environment secretary, Owen Paterson, told MPs: "If we do not take tough, and sometimes unpopular decisions, we will be putting at risk the success story that is the UK cattle industry. The UK's beef and dairy exporters have worked hard to develop markets valued at £1.7bn in 2011. We cannot afford to put such important and impressive industry performance at risk."

The shadow environment secretary, Mary Creagh, said: "This cull is based on hope not on science. We have warned the government for two years this cull will be bad for farmers, bad for taxpayers and bad for wildlife."

Campaigners opposed to the cull claimed the victory was only a political one. "Today's vote was about politics, not badgers," said Mark Jones, executive director of Humane Society International/UK. "We heard from many MPs unable or unwilling to vote against the party whip despite their conscience telling them a badger cull is unjustified. So our battle for badgers goes on in support of majority scientific opinion."

The National Farmers Union said the victory had settled "once and for all" the political debate. Meurig Raymond, NFU deputy president, said: "Today's vote is a ringing endorsement of the comprehensive strategy to bear down on TB and rid our countryside of this disease. Farmers are doing all they can to help prevent TB in cattle, but until we have a comprehensive strategy that bears down on the disease in wildlife, this disease will continue to run out of control."

The debate, at times ill-tempered, saw MPs contest whether the pilot culls, which are able to begin at any time in Somerset and Gloucestershire, would help curb the rise in bovine tuberculosis. More than 37,000 cows were slaughtered because of TB in 2012 at a cost to taxpayers of £100m. Creagh and Paterson agreed that the disease was the most pressing animal health problem facing this country, but the environment secretary insisted the cull was "one element of a comprehensive package, but an essential element" of TB control.

Creagh said: "The cull will cost more than doing nothing. If it works at all its effect will be marginal. It carries a real risk of making TB worse both in cattle and in badgers."

Anne McIntosh, a Conservative MP and chair of the environment, food and rural affairs select committee, whose report on Wednesday argued that vaccination was no a "magic bullet", said: "We are the only country to have given badgers legal protection and we have to live with the consequences of that." But Labour's Nia Griffith, MP for Llanelli, said: "Vaccination is the only way to put farmers in control." The Welsh government rejected badger culling in 2012 in favour of badger vaccination.

MPs supporting the cull said vaccination was too expensive but opponents quoted from an analysis reported in the Guardian that the high policing costs of the cull meant badger vaccination was now cheaper.

Green party MP Caroline Lucas said there was a need for even stricter controls on cattle movement to prevent the spread of TB. "Twenty-one percent of herds may harbour TB even after being cleared," she said. The shadow environment minister quoted John Bourne, the vet who led an earlier £50m badger culling trial, who told the Guardian: "It's an absolute nonsense that farmers can move cattle willy-nilly after only two tests."

Neil Parish, a Conservative MP from Devon, accused Labour of years of inaction while in government. "Farmers are at their wits end. We have to use every weapon that is there," he said. Daniel Kawczynski, another Tory from a mainly rural constituancy, praised Paterson for taking "a very courageous step".

But fellow Tory MP Tracy Crouch, who previously voted against the cull, said: "Some [colleagues] have barely spoken to me since." David Morris, another Conservative, said: "I am voting in favour of the cull through gritted teeth."

Liberal Democrat farming minister David Heath closed the debate and addressed the rising costs of the cull policy: "The only reason there will be policing costs is because some people are determined to break the law." He echoed many cull-supporting MPs in citing wildlife culls in other countries as having helped reduce TB in cattle.
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