Natura 2000 logging, Estonia

Forest clearcut and erosion at Haanja Nature Park, a Natura 2000 site. Credit: Siim Kuresoo. Location: 57.740076, 27.077508.

Page updated August 3, 2026
Considered the EU’s flagship conservation effort, the Natura 2000 site network is intended to protect Europe’s most valuable and threatened species and habitats to ensure their long-term survival.

Article 6.3 of the Habitats Directive requires an environmental impact assessment for any activities that are not necessary for Natura 2000 site management and that are likely to impact its conservation objectives, even if activities are outside the border of the site itself. The Estonian government, however, allows logging in Natura 2000 sites without performing impact assessments. In response, the European Commission sent a formal notice to Estonia in June 2021 requiring it to comply with its obligations. Continued violations prompted the Commission to send a reasoned opinion to Estonia in November 2023. Failure by Estonia to take measures to comply could result in a referral of the issue to the Court of Justice of the European Union.

However, the EU infringement proceeding process is known to be very slow and, in the meantime, valuable natural forests are being destroyed in Estonia. Thus in  2022, the FLC started working with attorneys Indrek Kukk and Liis Hääl (now at Tegos law firm) to support NGO Save Estonia’s Forest as it seeks a nationwide injunction prohibiting the Environmental Board from issuing logging permits in state-owned forests within the Natura 2000 sites unless the impact assessments required by the Habitats Directive have been properly performed and taken into account. If the case is successful, this should mean that NGOs no longer need to challenge individual logging permits (of which there are thousands each year).

The process of the case has been complicated. The Administrative and District Courts in Estonia initially rejected our claim because it wasn’t specific enough about the sites where the injunction should apply. However, in January 2024 the Supreme Court granted our appeal and confirmed that our request for an injunction was procedurally admissible provided that the claim was amended to identify specific Natura 2000 sites to be covered by an injunction. It directed us to file an amended claim to the Administrative Court for determination. Using geospatial data, we carried out an analysis of the forest habitats and forest-dependent species present in Estonia’s Natura 2000 sites that are likely to be adversely affected by logging activities. This analysis formed part of our amended claim which we submitted to the Administrative Court on April 5, 2024.

The Administrative Court again dismissed the claim in December 2024 on the basis of our claim being “insufficiently precise”, alleging that the coordinates provided of Natura 2000 site locations were incorrect and that specifying 441 different sites was “inadequate”.

In January 2025, we appealed the Administrative Court’s decision to the Tallinn Circuit Court. The Circuit Court was very slow to deal with the appeal, prompting us to submit a request for the Court to expedite the matter.

In October 2025, Tallinn Circuit Court granted our appeal, annulled the Administrative Court’s order dismissing our case, and sent the matter back to the Administrative Court for substantive proceedings. The Circuit Court’s reasoning was that:

• Our complaint adequately identified the forests by listing Natura 2000 sites by name and international code
• The exact coordinates are irrelevant, as our aim is to protect entire Natura 2000 areas, not specific points
• Our claim does not need to list individual cadastral parcels
• We have sufficiently demonstrated that the Environmental Board’s current practice of granting felling permits without proper Natura assessments is unlawful. On this point, the Court stated, “[t]he appellant has sufficiently substantiated its argument that the Environmental Board’s current practice in deciding whether to carry out the assessment (including preliminary assessment) referred to in Article 6(3) of the Habitats Directive for the granting of a felling permit in a Natura 2000 site is not in accordance with the purpose of that provision and is therefore unlawful.“

The case got substantive hearings between March and May 2026 that addressed the question at its heart: whether logging permits in Natura 2000 areas require proper environmental impact assessments in each case under Article 6 of the Habitats Directive.

As explained in guidance published by the European Commission, the Article 6.3 impact assessment process requires a documented preliminary assessment (“screening”) that determines if an activity is connected with or necessary to the management of the site, and whether it is likely to have a significant effect on the site. If an impact is likely, this triggers a full environmental assessment.

As part of the case, the Environmental Board disclosed documents laying out its approach to issuing logging permits, revealing that in the majority of permits, no preliminary assessment is conducted and logging operations are automatically classified as having no impact on a site.

Despite finding that the Environmental Board’s procedure was unlawful in some aspects, the Court dismissed our complaint on June 26, 2026.  The decision contained conflicting language on a number of issues, including whether a preliminary assessment is required.  We appealed the decision on July 27, 2026, and repeated an earlier request that the case be referred to the Court of Justice of the European Union, as it concerns questions of EU law (the applicability of the Article 6.3 requirement for preliminary assessments).