Agriculture & Farming UK-wide

Apply for a species licence from NatureScot

How to apply for a NatureScot species licence when your business activities could affect protected species in Scotland. Covers European Protected Species licences, the three derogation tests, application process, and what happens if you proceed without a licence.

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If your business activities in Scotland could disturb, capture, injure, or kill a protected species, or damage or destroy a breeding site or resting place, you need a species licence from NatureScot before you can lawfully proceed. Operating without a licence is a criminal offence.

This applies most commonly to construction and development projects, but also to forestry operations, infrastructure maintenance, agricultural land management, and demolition works. The licensing requirement applies regardless of whether you hold planning permission — planning consent does not override species protection law.

Scotland's species protection regime is separate from England and Wales. NatureScot is the licensing authority (not Natural England or Natural Resources Wales), and Scotland uses the 1994 Habitats Regulations rather than the 2017 Regulations that apply south of the border.

When you need a species licence

You need a NatureScot species licence if your activities could:

  • Disturb a European Protected Species (such as bats, otters, great crested newts, or beavers)
  • Damage or destroy a breeding site or resting place (such as a bat roost, otter holt, or badger sett)
  • Kill, injure, or capture any protected species
  • Disturb nesting birds on Schedule 1 of the Wildlife and Countryside Act 1981

Common triggers include building demolition (bat roosts), site clearance near watercourses (otters), excavation works (great crested newts), and tree felling (nesting birds and bat roosts).

Which species are protected

The species you are most likely to encounter on development sites in Scotland are bats (all species), otters, great crested newts, badgers, beavers, and nesting birds. Scotland is also a stronghold for species rarely found elsewhere in Britain, including the Scottish wildcat, pine marten, and capercaillie.

How to apply

The application process requires advance planning. You cannot apply retrospectively — the licence must be in place before you start work.

What happens if you proceed without a licence

Working without a species licence when one is required is a criminal offence. The consequences can be severe for both individuals and businesses.

Common problems and how to avoid them

  • Survey timing: Ecological surveys must be conducted during the correct season for each species. Bat activity surveys, for example, can only be carried out between May and September. If you miss the survey window, your project could be delayed by months.
  • Stale survey data: NatureScot typically accepts survey data that is 12 to 18 months old. If your project is delayed, you may need to commission updated surveys.
  • Incomplete applications: Missing information stops the determination clock. Ensure your ecologist provides all required supporting documents before submitting.
  • Starting work early: Beginning site clearance or demolition before the licence is granted is the most common and most serious error. Even preparatory works can constitute an offence if they disturb protected species.

What to do next

  1. Commission an ecological survey — appoint a suitably qualified ecologist to survey your site during the correct season
  2. Review the survey results — your ecologist will advise whether protected species are present and whether a licence is needed
  3. Apply to NatureScot — submit the application via the NatureScot Licensing portal at least 30 working days before you need to start work
  4. Wait for determination — do not commence any works until the licence is issued and conditions are understood
  5. Comply with licence conditions — ensure all works are supervised by the named ecologist and that a licence return is submitted after completion

Official guidance