Chiltern Railways wants to start a service between Oxford and London Marylebone via Bicester.
But a planning inspector said that works at Wolvercote tunnel would be harmful to the bats that use it as a flight corridor and to roost.
The company now has four weeks to work with Natural England to come up with a plan to protect the bat populations.
A spokesman for the secretary of state for transport told the BBC that once she was satisfied the bats could be protected, she would be likely to agree to the proposal.
Chilterns Railways and Natural England said they were working closely together and were confident that a solution to allow the development to continue would be found.
The common and soprano pipistrelle, the noctule and the Natterer’s bat are all thought to use the tunnel, which goes under the Wolvercote roundabout on the A40.