It’s a scene that Maria Ressa, a co-founder of an online news start-up critical of President Rodrigo Duterte of the Philippines, has grown accustomed to.

Late Wednesday afternoon, several plainclothes agents from the National Bureau of Investigations arrived in Ms. Ressa’s newsroom in Manila with a warrant for her arrest in a digital libel case involving her online news site, Rappler. An hour later, they took her and her lawyer away.

Ms. Ressa’s arrest is the most dramatic sign yet of Mr. Duterte’s crackdown on the news media in the Philippines. Mr. Duterte has not tried to hide his disdain for journalists, calling reporters “sons of bitches” and “spies” and even warning that they are “not exempted from assassination.”

As she left the building flanked by police officers, Ms. Ressa addressed reporters, telling them, “I will do the right thing.”

“These legal acrobatics show how far the government will go to silence journalists, including the pettiness of forcing me to spend the night in jail,” she later added in an emailed statement.

A judge initially denied bail to Ms. Ressa on Wednesday night, and she stayed in a conference room at the jail, editors at Rappler said. She was released after her lawyers posted bail for her on Thursday morning.

Chay Hofileña, a Rappler executive, said the arrest was “about media intimidation and media harassment.”

“This is proof,” she added, “because Rappler has been critical of the government, and they are very intent on silencing us.”

Ms. Ressa had already been served an arrest warrant and turned herself in to the authorities in December to face tax evasion charges. This time, the arrest warrant was related to an article that Rappler published in May 2012. In both cases, Ms. Ressa has called the charges “unfounded” and part of a larger attack on news outlets in the Philippines.