In a recent judgment, the Court of Justice of the European Union found that an administrative authority which rejects an application for a residence permit based on national law and, consequently, finds that the third-country national concerned is staying illegally on the territory of the Member State in question, must ensure compliance with the principle of non-refoulement, by reviewing, in the light of that principle, the return decision previously adopted against that national in the context of a procedure for international protection. 

"The Right to Seek Asylum: Interception at Sea and the Principle of Non-Refoulement", lecture by Prof. Guy Goodwin-Gill (Oxford)