Polish PM Mateusz Morawiecki attacked the EU institutions for exceeding their competences.
Brussels and Warsaw brought their years-long dispute to the European Parliament on Tuesday in a tense session in front of MEPs.
Their relationship was plunged into crisis earlier this month when a Polish court ruled some of Poland's laws had primacy of EU ones.
"We cannot and we will not allow our common values to be put at risk," said Ursula von der Leyen, president of the European Commission.
But Polish Prime Minister Mateusz Morawiecki, also present at the plenary session in Strasbourg, hit back.
"Poland will not be intimated," said Morawiecki, vowing to defend his country's sovereign independence against the "creeping expansion" of EU institutions.
The battle of words illustrated the poor state of relations between the two sides, which this month reached a new low after the Polish government endorsed a defiant judgment of the country's constitutional court that questioned EU law primacy.
The judges, in a majority decision, objected to the transfer of sovereignty from Poland to the EU and rejected the supreme legal authority of the EU's Court of Justice (ECJ), based in Luxembourg.
The ruling is seen as a "nuclear strike" on the primacy of the EU law, one of the union's cornerstone principles. Established back in 1964 as a result of the precedent-setting Costa v ENEL case, the principle states that, in all cases where the EU has competence, the bloc's laws have priority over national legislation, even over a country's constitution.
Von der Leyen used her speech to defend the principle.
"This ruling calls into question the foundations of the European Union. It is a direct challenge to the unity of the European legal order. Only a common legal order provides equal rights, legal certainty, mutual trust between member states and therefore common policies," she said.
"This has serious consequences for the Polish people. Because the ruling has a direct impact on the protection of the judiciary," she added. "Without independent courts, people have less protection and consequently their rights are at stake."
Von der Leyen reminded MEPs that the ruling followed years of threats to the independence of the judiciary in Poland, including the creation of a controversial disciplinary chamber to punish judges and remove them from office.
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