According to a statement released by Rappler, officials of the National Bureau of Investigation (NBI) on Wednesday afternoon served her a warrant, following which she was escorted to NBI headquarters.
Amnesty International Philippines said Ressa's arrest was based on a "trumped up libel charge".
Maria Ressa, who was selected by Time magazine as one of its Persons of the Year last year, was arrested over a libel complaint from a businessman which Amnesty International condemned as "brazenly politically motivated".
"This is what journalists in the Philippines now have to go through", she added. The article cited a Philippine intelligence report independent of the SUV case that tied Keng to drug trafficking - an accusation that could lead to death in Duterte's Philippines. He is supposedly close to lawmakers and had contacts with the U.S. embassy at the time. Rappler, founded in 2012, rejected the ruling.
The Cybercrime Prevention Act, however, did not become law until about four months after the story - which claimed that Keng owned the sport utility vehicle that the late chief justice Renato Corona used during his impeachment trial - was published.
Duterte had already banned a Rappler reporter from his news briefings after the government's corporate watchdog found that the news site violated a constitutional prohibition on foreign ownership of media when it received money from an worldwide investment firm.
Ressa rose to worldwide prominence in December 2018, appearing on an alternative cover of Time's Person of the Year edition. Duterte's government responded to the accolade by insisting that press freedom in the country remained "robust" and that Duterte "cannot intrude into that".
Rappler has drawn the administration's ire since publishing reports critical of Duterte's so-called war on drugs that critics say has targeted the poor and could amount to crimes against humanity. A year ago, Duterte's government revoked Rappler's journalist license and banned Rappler journalists from Malacanang, the presidential palace.
In a January 10 decision, the Department of Justice (DoJ) recommended that the Manila court indict Ressa and Santos.
The arrest was just the latest in a string of politically motivated cases filed against Ressa and Rappler.
"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", Ressa said in a statement.
Mr Duterte's spokesman said the charge against Ms Ressa was based on facts which she should simply answer and had "nothing to do" with press freedom. Rappler continued to publish on Wednesday, including covering Ressa's arrest, and the offending articles appear to still be available on the website.
Philippine journalist Maria Ressa, who has repeatedly clashed with President Rodrigo Duterte, was arrested in her Manila office on Wednesday in what rights advocates called an act of "persecution".