The Department of Justice filed the “grave threats” charge on Tuesday in a Quezon City court, spokesperson Polo Martinez said.
The case followed a National Bureau of Investigation (NBI) complaint filed in February 2025 over remarks Duterte made during a late-night news briefing.
Duterte had claimed she hired an assassin to kill President Marcos, his wife and his cousin, former congressman Martin Romualdez, if she were killed first.
Her lawyers argued on Tuesday that the criminal case should not proceed while she was facing impeachment.
“As a sitting impeachable officer, the Vice President may not be prosecuted for an alleged offense that is also the subject of an impeachment case,” defence lawyer Paul Lawrence Lim said.

However, Martinez said the Justice Department believed the criminal case could proceed alongside the impeachment trial.
“That’s correct,” he told AFP, adding that the case was now under the jurisdiction of the court.
University of the Philippines College of Law professor Dante Gatmaytan also said there was no legal barrier preventing the two cases from proceeding separately.
“This is not unconstitutional,” Gatmaytan said.
Under Philippine law, a conviction for grave threats carries a prison sentence of between one and six months. A separate complaint of inciting to sedition from the original NBI case has been dismissed.
Duterte was impeached in May over allegations that also include graft and corruption.
Tuesday marked Day 14 of her Senate impeachment trial, which could determine her political future.
A guilty verdict would remove Duterte from office and permanently bar her from holding elected office, putting her planned 2028 presidential bid at risk.
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