The RSPCA said it was a "black day for badgers", claiming the scientific case to support the mass slaughter of the animals had not been made.
Caroline Spelman, the Environment Secretary, acknowledged there was "great strength of feeling" about the issue but told the Commons: "I believe this is the right way forward."
More consultation will be carried out before any mass cull is allowed, but the Government plans to carry out a pilot in two areas.
The Secretary of State said badger control licences would be issued by Natural England under the Protection of Badgers Act 1992 to enable groups of farmers and landowners to reduce badger populations at their own expense.
If controlled shooting was found to be effective and humane, the policy could be introduced throughout England. Scotland and Wales set their own policy as disease control is a devolved issue.
Mrs Spelman hoped that her announcement would send a clear message to the farming industry, saying: "If culling is ultimately authorised, we will look to the farmers involved to show that they take their responsibility very seriously, and that they are committed to delivering culling effectively and humanely."
David Bowles, director of communications for the RSPCA, said: "Today is a black day for badgers - a day we have been dreading.
"At a time when the Welsh Government has stepped back from a cull, the Government in England is slowly shredding its own animal welfare credentials."
The RSPCA said vaccination of badgers, increased levels of testing, improved biosecurity and stricter controls on the movement of cattle were more effective ways of eradicating bovine TB in cattle for good.
Colin Booty, senior scientist for the RSPCA, said: "The RSPCA is sympathetic to farmers struggling to cope with the effects of this crippling disease and thinks that the problem of bovine TB in cattle needs a sustainable and effective solution.
"But this is not such a solution. We believe that the Government have taken the wrong fork in the road with this risky policy.
"This cull will contribute little or nothing to the long-term goal of eradicating TB nationally. Instead it will wipe out huge numbers of this much-loved species, including many animals which are healthy."
The Department for Environment, Food and Rural Affairs (Defra) said nearly 25,000 cattle were slaughtered in England last year because of bovine TB, which cost the country £90 million.
The problem is particularly bad in west and south-west England, where 23% of cattle farms were unable to move stock off their premises at some point in 2010 due to being affected by the disease.
Mrs Spelman said: "This terrible disease is getting worse, and we've got to deal with the devastating impact it has on farmers and rural communities.
"There's also the effect on the farming economy and taxpayers. Bovine TB will cost us £1 billion over the next decade in England alone if we don't take more action.
"First we need to stop the disease spreading even further. Then we need to bring it under control and ultimately eradicate it."
Investment in developing a TB vaccine was being made but there were "serious practical difficulties" with the injectable badger treatment, she said.
"I know that a large section of the public is opposed to culling, and that many people are particularly concerned about whether it will actually be effective in reducing TB in cattle and about whether it will be humane," she said.
"I wish there was some other practical way of dealing with this, but we can't escape the fact that the evidence supports the case for a controlled reduction of the badger population in areas worst affected by bovine TB.
"With the problem of TB spreading and no usable vaccine on the horizon, I'm strongly minded to allow controlled culling, carried out by groups of farmers and landowners, as part of a science-led and carefully managed policy of badger control."
Last week a key Government adviser said a cull would be a mistake.
Lord Krebs, who conducted a major review into badgers and bovine TB in the 1990s and recommended a trial cull which took place over the following 10 years, said he did not think it was "an effective policy".
He said research showed around a 16% reduction in new infections in herds following a badger cull, adding: "So you leave 85% of the problem still there, having gone to a huge amount of trouble to cull a huge number of badgers.
NFU president Peter Kendall said: "I join with farmers up and down the country today in breathing an enormous sigh of relief that the Government has shown leadership in tackling this terrible disease.
"This has never been about eradicating badgers; this is about eradicating disease.
"Today is a massive step forward and I thank Defra and the Secretary of State for the painstaking work that has gone into making what has been, I'm sure, a very tough decision in the face of not inconsiderable opposition.
"Sometimes we have to do what is unpopular because we know it is right. Not taking action is no longer an option and the Government has recognised that. As the most recent science shows, badger controls are absolutely necessary, together with cattle controls, to get on top of this devastating disease."
The English badger population was estimated to be 190,000 in 1995.
In the two planned pilot scheme areas - at least 150km squared - it is thought around 1,000-1,500 badgers would be culled over four years.
A nine-week consultation period will start, ending on September 19.
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