Critics say the ruling Law and Justice party is destroying Poland's democratic order by imposing excessive political control over the courts.
Thousands of people had gathered there the night before to protest the Law and Justice (PiS) party's reform, which came into effect at midnight.
Duda announced on Tuesday that Supreme Court president Malgorzata Gersdorf, a staunch critic of the reforms, had not asked for an extension and therefore would retire in line with rules introduced by PiS. CNN quoted her as saying, "My presence here is not about politics, I am here to protect the rule of law".
The other 26 judges forced off the bench by the new law also showed up for work Wednesday, according to PAP.
Their sentiments were matched by several worldwide organizations on Wednesday including Magistrats europeens pour la democratie et les libertes, an association of European judges and the global Bar Association's Human Rights Institute, who accuse Poland of ignoring the appeals of the worldwide judicial community and subordinating judiciary to executive power.
Additional reporting from Newsy affiliate CNN.More news: Thai Diver Dies During Cave Rescue Operations
The crowd chanted "Judges are not removable!" and "Constitution!" on Wednesday as the court's First President Malgorzata Gersdorf showed up for work, saying that according to the constitution, her six-year term runs through 2020.
The new law lowers the mandatory retirement age from 70 to 65 for the Supreme Court justices.
Through legislation and personnel changes, PiS has already taken de facto control of much of the judicial system since coming into power in 2015, including the constitutional tribunal and prosecutors, who now report directly to the justice minister.
"The constitution guarantees me this venerable post for six years, and I see no reason why I should file a petition with the executive branch about it", she said.
Ten judges have complied with the retirement legislation, a Supreme Court spokeswoman told AFP on Thursday.
The Supreme Court is the highest court of appeal for criminal and civil cases in Poland.More news: Scott Pruitt Steps Down From EPA
Since the conservative PiS came to power in 2015, the European Union has clashed repeatedly with Morawiecki's government over judicial reforms that have broadened the government's power over the Supreme Court and national council of the judiciary, which appoints judges.
"Many Europeans don't like the direction the European Union is going in", he said.
Their supporters say the law was aimed at certain judges and had little to do with age, an argument that was bolstered when the government named Justice Gersdorf's replacement: the 66-year-old judge Jozef Iwulski.
Pawel Mucha, an adviser to President Andrzej Duda, told reporters Ms Gersdorf's retirement results from the "force of law".
Polish Foreign Minister Jacek Czaputowicz said the law was binding and "for the time being our stance is that we are right". Unless Poland responds sufficiently to the EU's challenges, they could risk losing voting rights and funding.More news: Immigration enforcement is like liberating a town in combat: Donald Trump