Polish government spokesman Piotr Müller slammed the decision, which came a day after Germany’s Ursula von der Leyen was elected as the next president of the European Union’s executive arm.
"It is not a good situation that the European Commission is making such a decision in its old line-up,’ Müller said.
He added: “These are the last months of this Commission, and the new European Commission will start operating in November.
“It’s strange that such a decision is made the day after a new European Commission chief is elected."
The Commission started its procedure against Poland in April.
It argued that new rules have undermined the independence of Polish judges "by not offering necessary guarantees to protect them from political control."
It added that such guarantees were required by the Court of Justice of the European Union.
The Polish government was given two months to provide detailed explanations.
But the commission judged these to be unsatisfactory, and on Wednesday launched the second stage of its proceedings, formally calling on Poland to comply with EU law, state news agency PAP reported.
If the EU executive decides that Warsaw has failed to act, it can refer the case to the EU’s top court, PAP added.
Poland's governing Law and Justice party, which came to power in late 2015, has said that sweeping changes are needed to reform an inefficient and sometimes corrupt judicial system tainted by the communist past.
Poland’s prime minister argued in January that some of the legal changes made by his conservative government have met with criticism abroad because they are not understood in Western Europe.