Despite the appeal, the controversial changes were voted through by Poland’s lower house, amid cries of “shame” from opposition deputies. The amendments now go to the upper house for debate.
European Commission spokesman Christian Wigand earlier told reporters that Commission Vice President Vera Jourova had written to top Polish officials including the country’s president and prime minister, voicing concern over the draft law.
Jourova urged Poland to consult legal experts from the Council of Europe's Venice Commission before proceeding.
Polish government spokesman Piotr Müller told reporters in Warsaw that the European Commission’s appeal was “off the mark.”
Müller said the commission issued the appeal “not out of ill will, I hope, but simply because of a lack of reliable information.”
Poland's governing Law and Justice (PiS) party, which came to power in late 2015 and won a second term in power in October, has argued that broad changes are needed to reform an inefficient and sometimes corrupt judicial system marred by communist holdovers.
The changes have triggered a series of clashes between Warsaw and Brussels.
Poland’s prime minister said earlier this year that some of the legal changes made by his conservative government have met with criticism abroad because they are not understood in Western Europe.
Poland Supreme Court warned on Tuesday that the country may eventually have to leave the European Union as a result of plans by the ruling conservatives under which judges could be punished for questioning the legitimacy of the reforms.
Protests were held in dozens of towns across Poland on Wednesday by demonstrators critical of the planned legal changes.
Under draft legislation put forward by deputies from the ruling Law and Justice party (PiS), judges could face penalties for challenging the appointment of those of their peers who took up their posts after the conservatives came to power.
Some of the proposals were later modified during parliamentary work.
Prime Minister Mateusz Morawiecki has warned that if judges question the appointment or verdicts of other judges, the Polish justice system could be engulfed by chaos.
PiS politicians have said that rules similar to its proposals exist in other countries, France in particular.