Poland is facing the prospect of an unprecedented institutional crisis, amid escalating tensions between its nationalist government and the EU.

Thousands of people took part in anti-government protests in Warsaw and several other Polish cities late Tuesday, after the country’s ruling Law and Justice party (PiS) implemented legislation that could force as many as one-third of the top court’s sitting judges to step down.

Nonetheless, despite judicial reforms effectively forcing her to retire, Poland’s Supreme Court chief justice took a defiant stand against President Andrzej Duda on Wednesday.

Less than 24 hours after vowing to fight to protect the constitution and the independence of Poland’s courts, Malgorzata Gersdorf returned to work at Warsaw’s courthouse building on Wednesday morning.

Surrounded by hundreds of cheering supporters, Gersdorf told reporters: “My presence here is not about politics. I am here to protect the rule of law.”

On Tuesday, PiS implemented legislation to lower the mandatory retirement age for justices to 65 from 70. They also called for a disciplinary chamber to be established, stoking fears the right-wing administration could soon use the directive to intimidate judges.

Under the new rules, Gersdorf — who is 65 years old — was required to ask Duda for an extension of her mandate from Wednesday. However, she refused to seek permission from Poland’s president to continue as the country’s top judge, reportedly saying this would constitute “subordination.”

Through legislation and personnel changes, PiS has sought to assume de facto control of the nation’s judicial system since coming to power in 2015. This includes radical changes to Poland’s constitutional tribunal and prosecutors — who now both report directly to the justice minister.

Poland’s government argues such changes are necessary in order to help combat corruption and improve the court’s efficiency.

At the start of the week, the European Commission opened a fresh legal case against Poland, saying recent changes to Poland’s legislation had undermined its judicial independence.

The ongoing conflict has isolated Poland within the EU, while also exposing the bloc’s apparent inability to rein in governments that contradict its core democratic values.

Meanwhile, under a separate legal procedure launched by the EU late last year, Warsaw has found itself in danger of losing its voting rights in the bloc. Hungary, another country in the EU facing intense criticism over democratic standards, has pledged to block this move.

“The tense Warsaw-Brussels relations may further boost euroskeptic sentiment in Poland, especially in the run-up to the presidential and parliamentary elections in May and October 2019, respectively,” Otilia Dhand, senior vice president at Teneo Intelligence, told CNBC via email.