Environment Secretary Owen Paterson told the BBC "badgers moved the goalposts" when he was asked why the pilot cull failed to reach its target.
A badger cull in west Somerset has been extended in a bid to make up for the shortfall.
When asked why he had "moved the goalposts" and claimed the cull was a success, Mr Paterson said: "The badgers moved the goalposts.
"We're dealing with a wild animal, subject to the vagaries of the weather and disease and breeding patterns."
A decision on whether to extend the badger cull in Somerset is expected later this week.
Natural England is considering an application from the culling company involved.
This morning Defra has revised its badger population estimates:
Number of badgers in each area
- 1450 in Somerset (compared to initial estimate of 2400 in September 2012)
- 2350 in Gloucestershire (compared to initial estimate of 3400 in September 2012)
With these revised figures, Defra says the minimum number of badgers needed to be culled is:
- 1020 in Somerset
- 1650 in Gloucestershire
In the six weeks of the cull, 850 badgers have been removed in Somerset.
Musician and wildlife campaigner Brian May says the badger cull is morally wrong following calls for the trial to be extended.
It's estimated 850 badgers have been killed - far short of the target of more than 2000. Defra and Natural England say extending the cull will maximise disease control benefits.
A pilot badger cull is set to be extended by up to three weeks because fewer animals were killed than had been hoped.
Defra said Natural England was considering an extension to the west Somerset cull to "maximise the disease control benefits".
According to reports, just 850 badgers have been shot in the area over the six-week trial, just over 40 percent of an initial target of 2,081. The aim was to kill 70 percent of badgers in west Somerset and Gloucestershire by free shooting.
A Defra spokesman said: "Early indications suggest that the Somerset cull has been safe, humane and enough badgers have already been killed to help reduce bovine TB.
"Natural England is currently considering an application from the cull company for a short extension of two to three weeks so as to maximise the disease control benefits achieved this year."
The Government said a Daily Telegraph report that thousands of homes would be made to install water meters was untrue.
Defra released the following statement:
There is no requirement for water companies to introduce compulsory water meters as a result of the report that has just been published.
In fact, the number of water companies labelled as seriously water stressed was reduced. Metering is just one of many ways water companies look at to manage water resources in their area.
The Government is doing more than ever before to tackle water prices, securing a £50 rebate off the exceptionally high bills of those in the South West, bringing in social tariffs for the first time and, through our Water Bill, bringing in competition for all non-household users.
The Government said a report that it plans to introduce compulsory water meters for millions of householders "is false".
Defra said in a statement of the Daily Telegraph report: "Any suggestion that this has made it more likely that customers will face compulsory water metering is not true.
"No water company is required to introduce compulsory metering, even if it is in an area of severe water stress".
Millions of families in Britain could face higher bills under new government plans to install compulsory water meters in homes, the Daily Telegraph has claimed.
The Environment Secretary, Owen Paterson MP, this week approved plans to make water companies across a third of the UK fit meters and bill customers for usage.
Ministers have warned that reservoirs are at risk of running dry due to water shortages.
Facebook.com attracted 4.1 million page views and bbc.co.uk 2.8 million at DEFRA between January and June this year, a FOI request suggests.Read the full story ›
Defra are considering plans that could see badgers given an oral contraceptive pill to curb numbers in the ongoing debate about the badger cull.
The move is one possible alternative to culling put forward to control the spread of TB over concerns the infection passes from badgers to cattle.
Other lethal and non-lethal strategies are also under review.
The Prince of Wales and Prince William are to host a conference later today which will call for a global partnership to stop the illegal trade in wildlife.
Wildlife losses have reached unsustainable levels, with tens of thousands in some places, the World Wide Fund for Nature said.
It added that the world is currently faced with an "epidemic" of poaching and trafficking of illegal wildlife products, caused by an increase in demand, particularly from south-east Asia.
The conference, in conjunction with Defra will be the first stage in a process which will result in key countries signing a declaration at a meeting this Autumn, to end the illegal trade in wildlife.