Rappler, founded in 2012 as a scrappy investigative and entertainment outlet, has been a main target of his verbal abuse. Its star political reporter, Pia Ranada, in particular has been singled out. At one news conference, Mr. Duterte warned her not to go to his hometown, Davao, where he was once mayor, because “something bad will happen to you.”

Earlier this year, Ms. Ranada was stripped of the press pass that allows her to cover Malacañang Palace, the Philippine equivalent to the White House. Rappler reporters have been barred from covering any official presidential events. Such treatment has alarmed media groups.

“More than his inability to tolerate dissent, Duterte’s relentless persecution of the media appears to be part of the increasingly authoritarian direction his presidency has taken,” the National Union of Journalists of the Philippines said in a statement on Sunday night.

Rappler’s newsroom has also been on the front lines of a war against misinformation on Facebook, where most Filipinos get their news. Rappler reporters have been the targets of online death and rape threats so severe that senior editors have debated installing bulletproof windows in the news organization’s office.

This year, Rappler became an official fact checker for Facebook, which has called the Philippines “Patient Zero” in the battle over misinformation.

The Philippine government’s case against Ms. Ressa and Rappler was brought by the country’s Department of Justice and centers on a 2015 investment in Rappler by the Omidyar Network, an American organization owned by Pierre Omidyar, the founder of eBay. At the heart of that case is a financial transaction that is also the subject of a Philippine Securities and Exchange Commission effort this year to revoke Rappler’s license to operate.

The charges treat Rappler as though it were a “dealer in securities” and not a news organization, Ms. Ressa said, adding that Rappler has paid the right taxes required of a news organization in the Philippines.