Conservative MP Owen Paterson said that, if successful, the cull aimed at stopping bovine tuberculosis would be rolled out across the country next year.
It has not been confirmed where this summer’s pilot culls will take place, however the National Farmers Union (NFU) said it believed they would be in Gloucestershire and Somerset.
Animal rights campaigners expressed dismay, claiming there is still no scientific evidence to support the cull and that the move is against the wishes of the British public.
Speaking to the BBC, Mr Paterson said: “We need to make sure that these two trials are carried out in a professional and scientific manner and if we prove that this works we will continue.”
The Government wants to stop the animals spreading the disease which has cost the taxpayer £500m in the last decade. That figure is expected to rise to £1bn in the next 10 years
The cull was originally scheduled last autumn but was cancelled at the last minute after a series of problems, including finding more badgers than anticipated in the areas which had been selected for the trials.
But Mr Paterson assured farmers from across the South West that the planned action, which will see the animals shot by trained marksmen, will go ahead at the earliest opportunity.
Adam Quinney, the vice president of the National Farmers' Union, welcomed the decision and said they had expected the cull to go ahead this summer.
“The two licences have been issued for two areas in Gloucestershire and Somerset and they still stand.
“There have been discussions about looking at alternative areas just because it is prudent," he said.
A spokeswoman for The Department for Environment, Food and Rural Affairs (Defra) confirmed: “The earliest the cull can take place is from June 1, and it will definitely be going ahead this summer.”
A spokesperson for a national animal protection organisation said they were “deeply disappointed” with the plans to cull the animals tomorrow as there is no “real proof” that it will help either cows or badgers and called for Defra to look again at alternatives including vaccines.
They said: “The Government must think again.
"After this year's postponement we had hoped that the government would finally see sense and pay attention to the vast amount of scientific research showing that a cull will be ineffective, wasteful and potentially damaging to the welfare of both farm and wild animals.
"The vaccination of both badgers and cattle along with more effective biosecurity is the only approach which addresses the welfare of both cattle and badgers and the long term livelihood of farmers.
"This announcement flies in the face of the views of a huge majority of MPs who voted against the cull as well as the majority of the British public and the overwhelming weight of scientific opinion."