Ressa, the chief executive of Rappler and a 2018 Time Person of the Year, called the accusation an attempt by Duterte's government to silence the publication, CNN reported.
She was formally arrested at Rappler's headquarters in Manila after being served an arrest warrant by Philippines National Bureau of Investigation (NBI) officers. Footage streamed on Facebook showed plainclothes officials speaking to the journalist, while several of the site's journalists live-streamed on Facebook and Twitter what was happening.
They were reportedly asked by the NBI to stop filming and taking photos.
Ressa has been indicted multiple times on libel and tax evasion charges described by critics as politically motivated and designed to silence independent media in the country.
According to reports, the latest charge against the journalist stemmed from a May 2012 report on a businessman's alleged ties to a former judge in the Philippines' top court.
The case comes under a controversial "cyber-libel" law, which came into force in September 2012, four months after the article in question was published.
Officials first filed the case against Ressa in 2017, but it was dismissed by the NBI because the one-year limit for bringing libel cases had lapsed. However, in March 2018, the NBI reopened the case.
The news website has reported extensively on Duterte's brutal war on drugs which earned praise from human rights advocates. But it made the site and its journalists a target of supporters of the Duterte administration.
Duterte's office denied the President's involvement in the prosecutions against Rappler, but he previously sparred with the company's employees that led to him banning Ressa and reporter Pia Ranada from Malacanang Palace, his official residence, over their coverage of his administration.