Defra carried out pilot culls in West Somerset and Gloucestershire in 2013 to halt the spread of bovine tuberculosis.
A full roll-out is being considered after more culls in the same regions.
But the trust says it would be unlawful due to a lack of "any independent monitoring". It hopes the legal challenge will be heard in July.
The charity believes culling will not stop TB from being spread and could make it worse.
An independent panel of experts was appointed to report to ministers on the badger culling pilots in 2013 to assess the safety and humaneness of the operation.
The government has not put one in place for the second stage of culls planned for later this year, opting instead to use its own bodies, Natural England and Animal Health and Veterinary Laboratories Agency.
But a trust spokesman said without it "there can be no proper assessment" which would be needed "before any lawful decision to continue with further culls around the country".
"Owen Paterson [the environment secretary] has done all he can to prevent this judicial review case going to the High Court and he has failed," said Dominic Dyer, from the Badger Trust.
"His refusal to put in place any independent monitoring of the badger culls is a national disgrace."
A Defra spokesman it would "not be appropriate to comment on ongoing legal proceedings" but said "doing nothing" was not an option and culling badgers was "one part of our broad strategy to rid the country of this terrible disease".
The Badger Trust has been granted permission for a judicial review to challenge the government's plans to continue culling badgers this year.