The county plans for Harju and Rapla Counties remain in force.

According to the Administrative Chamber of the Supreme Court, the minister of public administration endorsed the Pärnu County plan in violation of the law, as the impact to be exerted by Rail Baltic on Luitemaa Nature Reserve situated next to the track had not been established. A Natura assessment must always be carried out if it cannot be ruled out on the basis of a preliminary assessment that the planned activity will have a significant impact on the objectives of of protection of Natura areas, the top court said.

The two non-governmental organizations (NGOs) that challenged the county spatial plans for the Rail Baltic track argued in their action, originally filed with an administrative court, that the county plans were illegitimate due to both procedural violations as well as on substantive grounds.

The two organizations said that an existing rail corridor should have been chosen for Rail Baltic. The organizations also found that no proper attention was given to finding out about the environmental condition of the proposed new track corridor and the railroad's impact on the natural environment, including protected bird species.

In July 2019, Tallinn Circuit Court dismissed an appeal by the NGOs and did not change the decision to dismiss the NGOs' action made by the administrative court on September 7, 2018.

The top court did not, however, accept an appeal concerning the endorsement of the same county plans filed by a third nonprofit, the Estonian Geographical Society (EGS).

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