Duterte accused Supreme Court Chief Justice Maria Lourdes Sereno of corruption and alleged the ombudsman, Conchita Morales, was conspiring with opposition figures to bring down his government.
Morales's office has been investigating allegations that Duterte had secret bank accounts that recorded millions of dollars he embezzled while a long-time mayor of the southern city of Davao.
"In the end, to their sorrow, they will discover that there is no such thing as that amount," Duterte said of the alleged embezzled millions, telling reporters his net worth was just 40 million pesos (around USD 784,000).
The council confirmed last week that it was evaluating the ombudsman's request to investigate Duterte's bank accounts, and on Tuesday Morales vowed to pursue the case.
Duterte accused Morales of being aligned with former president Benigno Aquino and other opposition figures.
"They all want to force me out of Malacanang (the presidential palace)," he said.
Duterte said today he would also file an impeachment case against Sereno for allegedly failing to disclose earnings when she was a lawyer, as required by law of all public officials.
A majority of senators support Duterte but they have also shown this year they will not endorse everything he does, and they may not back his impeachment moves.
However opponents have said Duterte's campaigns against Sereno and Morales are part of his scorched-earth tactics meant to destroy the credibility of his critics.
Edcel Lagman, an opposition congressman, accused Duterte of trying to "wreck democratic institutions".
Duterte last year vowed to "destroy" Senator Leila De Lima, one of the chief opponents of his controversial war on drugs that has claimed thousands of lives.
De Lima insists the charges were trumped up to silence her. Rights groups and European lawmakers call De Lima a political prisoner.
Duterte has similarly vowed to destroy Senator Antonio Trillanes, one of his other chief critics who first raised the allegations he had secret bank accounts.
Duterte, who frequently uses crude language, today said Trillanes had one testicle and alleged he was having an affair.
Duterte's allies in congress last month voted to defund the Commission on Human Rights because of its focus investigating alleged extrajudicial killings in the drug war. Duterte branded the head of the commission a paedophile.
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