English Nature have recently published a review of how local authorities deal with protected species in the planning system. It makes very interesting reading.
"Development control, local authorities and protected species" - can be viewed here.
In particular I would draw your attention to the following conclusions:
"... the principal of pre-determination surveys should become more firmly established".
"... a more structured and consistent approach to dealing with protected species in development control is likely to lead to financial and time savings for both applicant and local authority, as well as better conservation of protected species and their habitats."