Only a quarter of the badgers in two pilot cull areas were killed in the way the schemes were designed to test, official figures have shown.
The revelation that only 24% of the badgers in the two areas were culled using "controlled shooting" - shooting free-running badgers - in the original six-week culls has prompted criticism of Government claims that the pilots were a success.
The two pilot culls in the West Country were run to see if controlled shooting coul d be done safely, humanely and effectively as part of a programme to reduce bovine TB in cattle herds.
Previous studies have shown that, to be effective in reducing the disease in herds, culling had to remove 70% of the badgers - which can spread bTB to cattle - in an area.
But a freedom of information (FOI) request has revealed that in the West Somerset pilot just 360 badgers, some 25% of the total estimated population of 1,450 in the area, were killed by controlled shooting in the original six-week period of the cull.
Far more - 490 badgers - were trapped in cages and shot in that time.
And in West Gloucestershire 543 badgers were killed through controlled shooting in the six-week period, 23% of the 2,350-strong population, while 165 were cage-trapped and shot.
The pilot culls have already been criticised for not being effective, as the overall number of badgers killed fell short of the 70% benchmark in both areas.
In West Gloucestershire just 30% of the estimated population was killed in the six-week period and in West Somerset the figure was 60%. Both culls were extended and in total 40% of badgers were killed in Gloucestershire and 65% in Somerset.
Critics of the cull, who claim it is not an effective way of reducing bTB in cattle herds and is inhumane, said the breakdown of the figures for methods of culling further undermined claims by Government that the pilots were successful.
Dominic Dyer, policy adviser for wildlife charity Care for the Wild, said: "The pilot culls were designed to test that controlled shooting was a safe, humane and effective means of reducing 70% of the badger population in the two areas.
"They actually only managed to reduce 24% by that method. Any suggestion the culls were a success is therefore grossly misleading."
He also raised concerns that the Government did not give the information on a breakdown of methods used to cull badgers when requested by Green MP Caroline Lucas, even though the figures had been revealed in the FOI some days earlier.
Answering a written question by Ms Lucas last year, Farming Minister George Eustice said: " Further details on the method used to remove badgers will be released in due course once analysed by the independent expert panel."
Mr Dyer said: "This is vitally important information that has been swept under the carpet or hidden by political sleight of hand.
"Owen Paterson has claimed that the culls were a success because in Somerset they 'killed 60%' of the badgers. But he doesn't admit that the majority of these were killed by trapping and shooting - which was not what these trials were meant to test."
Relying more on cage-trapping to meet the 70% target could also push up costs of the cull.
The Environment Department's (Defra) impact assessment, estimating the costs of each culling area as being £4.5 million, was based mainly on controlled shooting, with some use of cage-trapping.
Controlled shooting was estimated as costing just £300 per square kilometre per year, and cage trapping and shooting would cost £2,500 per square kilometre per year. A combination was estimated at £1,000 per square kilometre per year.