The Luxembourg-based Court of Justice of the EU said the new disciplinary chamber set up at Poland's Supreme Court "does not provide all the guarantees of impartiality and independence, and, in particular, is not protected from the direct or indirect influence of the Polish legislature and executive".
The ECJ had already told Poland to immediately stop all proceedings at the disciplinary chamber - set up by the ruling nationalists as part of their sweeping overhaul of the judiciary in recent years - to prevent damage before the main ruling.
Poland's top court, however, said on Wednesday that the ECJ's interim measures imposed on the Polish disciplinary chamber contravened the Polish constitution and that Poland should therefore not follow them, a ruling that challenges a key EU tenet of primacy of European laws over national ones.
That does not mean Warsaw must now follow in Britain's footsteps and trigger the formal EU divorce procedure but is undergoing a de-facto "legal Polexit of the judiciary", an EU official said, moving itself further away from the bloc.
Polish opposition parties say the process could ultimately lead to the country leaving the EU.
Separately on Thursday, the bloc's executive European Commission was starting new legal cases against Warsaw and Budapest for violating LGBT rights, according to a document seen by Reuters ahead of its official release later in the day.
The Brussels-based executive, which acts as the guardian of EU laws across the 27 member states, will take Poland to task for not addressing concerns around some areas in the country that declared themselves "LGBT-free zones".
Hungary touched a raw nerve in the bloc in recent weeks with a new law that bans from schools materials deemed as promoting homosexuality, which many in the EU see as restrictive, discriminatory and infringing on LGBT and human rights.
(Reporting by Gabriela Baczynska; editing by John Stonestreet and Philippa Fletcher)