Birdwatchers have spotted barn owls and skylarks on the site at Throckmorton airfield, near Pershore. Both species are protected by European directives and the Wildlife and Countryside Act, which makes it an offence to disturb their nests during the breeding season.
Jack Hegarty, head of planning at Wychavon DC, said the birds' presence could derail the Home Office's plan.
'It could be a showstopper', he said. 'We want to involve wildlife trusts and English Nature but we don't know the full extent of the ecological concerns until there's a public discussion. As a council, we've made it clear that we don't believe this is the right site'.
A Home Office spokesman commented: 'We are poised to submit planning notification. An environmental assessment, including an ecological survey, will be submitted as part of that process'.