Although the taking and storing of fingerprints in passports constitutes an infringement of the rights to respect for private life and the protection of personal data, those measures are in any event justified by the aim of protecting against any fraudulent use of passports.
However, the Court also notes that the regulation explicitly states that fingerprints may be used only for verifying the authenticity of a passport and the identity of its holder. Moreover, the regulation does not provide for the storage of fingerprints except within the passport itself, which belongs to the holder alone. The regulation not providing for any other form or method of storing those fingerprints, it cannot in and of itself be interpreted as providing a legal basis for the centralised storage of data collected thereunder or for the use of such data for purposes other than that of preventing illegal entry into the EU.
The Court of Justice of the European Union has ruled that the inclusion of biometrics (two fingerprints) in passports is legal. See their press release with links to additional documents here.
The ruling was not unexpected, but is still a blow to privacy advocates in the EU who opposed the use of biometrics in passports.
Update: A reader submitted two media reports on the ruling that may be of interest to you all: