Presidential aide Pawel Mucha dismissed Gersdorf's remarks and told reporters Gersdorf was "going into retirement in accordance with the law", and insisted the Supreme Court was now "headed by Judge Jozef Iwulski", who was chosen by the president.
Renowned for her iron will, the blond, bespectacled 65-year-old has refused to comply with a new law that reduces the retirement age for Supreme Court judges from 70 to 65, arguing that the six-year term she is guaranteed under the constitution ends in 2020.
The new law retired more than a third of the Supreme Court's 82 judges, a move widely seen as an attempt by the ruling Law and Justice party to take control over the judiciary.
Polish Prime Minister Mateusz Morawiecki told the European Parliament on Wednesday that EU countries have the right to shape their courts according to the own traditions. "To a large extent, the independence of Poland's constitutional court has been destroyed".
Two separate letters, signed by MEPs across the political spectrum and former Polish leaders, demand that the Commission take swift action to halt a controversial judiciary reform in Poland, already closely watched by Brussels for fears that it threatens the basic democratic rules.
Gersdorf said Tuesday that she will "go on vacation" after showing up at work on Wednesday.
Its executive European Commission launched another rule-of-law procedure this week against Poland. It forces the retirement of about 40 percent of the Supreme Court's justices - 27 out of 73.
"What if I have a court case against someone from PiS and they will be able to influence judges".
An adviser to President Andrzej Duda also insisted that Gersdorf has no choice but to step down.
Their sentiments were matched by several global organizations on Wednesday including Magistrats europeens pour la democratie et les libertes, an association of European judges and the worldwide Bar Association's Human Rights Institute, who accuse Poland of ignoring the appeals of the global judicial community and subordinating judiciary to executive power.
Hundreds of people demonstrate to support the Polish Supreme Court Justice president in front of the Supreme Court building in Warsaw.
Besides Warsaw, demonstrations have also been held in several other Polish cities in defense of the country's constitution. The domestic upheaval as well as concerns by the European Commission prompted authorities to concede to some changes, though the main thrust of the legislation has remained the same.
"Its decision will be very important for the European Union because it will define the extent to which European Union law can interfere in the autonomy of member states in the way they organise their judicial systems", Szymanski told AFP.
He also said he was ready to "lead a physical removal of the main perpetrator of all misfortune", referring to PiS leader Jaroslaw Kaczynski.
Unless Poland responds sufficiently to the EU's challenges, they could risk losing voting rights and funding.
Brussels in December triggered so-called Article Seven proceedings against Poland over "systemic threats" to the rule of law, which could eventually see Warsaw's European Union voting rights suspended.