David Cameron has acknowledged that the proposed badger cull trials would involve “no end of difficulties”, including concerns over policing.

The Prime Minister insisted the two pilot schemes aimed at controlling the spread of bovine TB, likely to take place in the South West, were the “right thing to do” despite the concerns of wildlife campaigners. Mr Cameron, commenting on the policy for the first time since it was given the go-ahead, said that those protesting against the decision to cull badgers were forgetting that the species was also suffering from the “terrible” disease.

In an interview with BBC One’s Countryfile, Mr Cameron said the situation was “very difficult” but “what we want is healthy cattle but we also want healthy badgers and I think sometimes the critics of the culling trials forget that in the end it’s the badgers who are also suffering from this terrible disease as well”.

He added: “I think it’s right to take this difficult step to have these pilots – we’re going to have to watch very closely about how they’re put in place, how they’re carried out, but in the end the aim is healthy cattle, healthy badgers.” Ministers hope culling will lead to a reduction in bovine TB by 16 per cent. The disease, carried by badgers, led to 25,000 cattle being slaughtered in England last year, most in the South West.

Six-week trials will take place in two areas later this year and could lead to a wider cull across the country as part of efforts to tackle TB in cattle. Ministers will choose from a shortlist of potential cull areas to be drawn up this month. Devon or Cornwall and Gloucestershire are thought to be the front-runners.

Next month’s National Farmers’ Union conference, which will be addressed by Environment Secretary Caroline Spelman, is set to be targeted by animal rights protesters angry at the proposed culls, and with feelings running high Mr Cameron acknowledged the trials could be difficult to police.

He acknowledged “it’s going to be controversial, it’s going to be a difficult thing to do”.

The trials will be “difficult to police, difficult to carry out, there’s no end of difficulties, but the question we faced as a Government is when you’ve got all this evidence that culling should be part of – only part of – a balanced package of measures, do you just sweep it under the carpet and announce another review or do you say OK, we need to get on and see if we can make this work?

“And we’ve taken the difficult decision and I think that’s the right thing to do.”

Mr Cameron also used the interview to repeat his pledge to allow a vote on repeal of the Hunting Act in this Parliament. He said: “I always thought the hunting ban was a pretty bizarre piece of legislation, I think there should be a free vote in the House of Commons, I think that the House of Commons should make its mind up about this. My problem has always been that it was just taking the criminal law into an area of activity where it didn’t really belong.”

Police forces risk being landed with a multi-million-pound bill to prevent badger culls from causing deep unrest in the countryside.

Policing the targeted shooting for the full four years of a cull could cost £2 million, official estimates show.

If the pilots prove successful, the Government is considering giving out licences for ten four-year culls, meaning the bill could spiral to £20 million. The Department for the Environment, Food and Rural Affairs has said it would share policing costs with the Home Office – but the breakdown is unlikely to be 50-50.