Chiltern Railways says it is "disappointed" plans for major improvements to rail services in Oxfordshire and Buckinghamshire face new delays because of a row over bats.
The company has been told a public inquiry into its scheme to run services from Oxford and Bicester to Marylebone for the first time is to be re-opened.
It will again look at the impact the new service will have on bats in a tunnel at Wolvercote following concerns from animal groups along with other concerns.
The project called Evergreen 3 will mean more services to London and create a direct link between Oxford with Marylebone.
New track will be laid between Bicester and Oxford to allow the new line.The inquiry will open later in the year.