Justice Maria Lourdes Sereno gave the warning as legislators in the House of Representatives prepared to begin impeachment hearings against her following a threat by Duterte that Sereno would be forced out.
Sereno has been one of the few voices willing to criticise Duterte for allegedly disregarding due process and attacking other branches of government as part of his brutal anti-crime campaign.
Duterte in turn vowed last month to impeach Sereno for alleged corruption. His allies in Congress will begin hearings on the impeachment complaint this week.
"This is getting to be larger than myself. This is no longer just about me. It is about democracy," Sereno told broadcaster ABS-CBN in a live interview.
Philippines Duterte says only answers to his people on drugs war, human rights
She said the charges against her were fabricated and warned that the judiciary would be under threat if the Duterte government was allowed to pursue her. "Is the judiciary safe? And if the judiciary is not safe, is democracy safe? Are the constitutional rights of people still assured?" she asked.
Earlier this year Duterte's arch-critic, Senator Leila De Lima, was arrested on charges of drug trafficking and is behind bars awaiting trial. De Lima insists the charges were trumped up to silence her. Rights groups and European lawmakers call her a political prisoner.
Duterte has also called for the impeachment of government Ombudsman Conchita Morales after her office began investigating allegations that Duterte had secret bank accounts containing millions in embezzled funds.
Elected last year on a promise to wage a bloody war on drugs, Duterte has been accused of tolerating human rights abuses and ignoring the rule of law as he pursues suspected drug users.
The government says almost 4,000 "drug personalities" have been killed by authorities as part of Duterte's campaign but critics say thousands more have died at the hands of government-backed vigilantes.
Duterte enjoys widespread support and his allies control both houses of Congress. But concern is growing that he is seeking to monopolise power through his attacks on independent branches of government.
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