2 Strict Nature Reserves have been separated in the Park – Plokštinė and Rukundžiai Reserves. No forestry, agriculture or any other type economic activity is permitted in the strict nature reserves. Gathering of forest products, hunting and educational tourism are not permitted here. Only visitors having scientific purposes are allowed to visit these locations if they have permits, issued by the Administration of the ŽNP.
Plokštinė reserve is aimed to preserve standard complex of Plokštinė woods and marsh with ecosystems typical for this region, rare species of plants, mushrooms and animals, natural streams of Juodupis and Uošna and unique geomorphological structure of Plokščiai thermo-sinkhole.
Rukundžiai reservation preserves the unique natural complex of marshy woods of Aklaežeris and the stream of Pietvė.