Almost 30 opposition lawmakers also faced criticism for failing to appear in parliament for an initial vote on whether to put the legislation on the agenda for the day.
Commission spokesman Christian Wigand told a regular news briefing that Commision Vice President Vera Jourova had written to Polish authorities on Thursday expressing concern about the draft law.
The spokesman for the United Nations human rights office, Rupert Colville, also on Friday expressed "concern" over the draft legislation, which he said "risks further jeopardising the independence of the judiciary in Poland". Saying the commission was concerned about judicial independence and rule of law, she asked Polish authorities to consult with legal experts at the Council of Europe, the continent's leading human rights body, before moving forward.
The Council of Europe's Commissioner for Human Rights, Dunja Mijatovic, also called on parliament to discontinue work on the "bill now being rushed through". It argues the changes make the system more efficient.
Defying Brussels, Poland's parliament on Friday passed a law punishing judges critical of controversial court reforms, a measure the governing conservatives say is necessary to avoid judicial chaos but that the opposition calls a threat to the rule of law.
The EU has been accusing the PiS of politicising the judiciary since the party came to power in 2015.
Protesters gathered in large numbers across Poland on Wednesday evening to denounce legislation being pushed by the populist ruling party that would give the government the power to fire judges.
Among other items in the draft law, which the lower house will begin debating Thursday, the government would have the power to discipline judges who carry out rulings in line with European Union law, including questioning judicial appointments.
The U.N. High Commissioner for Human Rights on Friday said the legislation "risks further undermining the already heavily challenged independence of the judiciary in Poland". A heated debate took place on Thursday, with a parliamentary commission working all night and making some changes. Many feared that Poland might be forced to leave the European Union because it would put the Polish government's wishes above European Union law at risk.
The EU's top court said last month it was up to Poland's Supreme Court to decide whether the panel was independent, and the Supreme Court has ruled that in its view the panel was neither impartial nor independent.