Campaigners for press freedom have expressed alarm after authorities in the Philippines said they would file charges of tax evasion against a news website that has been an outspoken critic of the country’s authoritarian president, Rodrigo Duterte.

The US-based Committee to Protect Journalists said on Sunday it was “extremely concerned” about the threat to indict the major news site Rappler and its president, Maria Ressa, calling the charges “a direct assault on press freedom in the Philippines”.

The country’s justice department said it found probable cause to indict Rappler Holdings Corp and Ressa. The case could be filed later this week, the justice secretary, Menardo Guevarra, said on Sunday.

Rappler called it “a clear form of continuing intimidation and harassment” and an attempt to “silence reporting that does not please the administration”.

“Rappler has distinguished itself with in-depth investigative reports into stories, such as extra-judicial killings, that have been highly critical of the government, and there’s every reason to believe the charges are politically motivated,” the CPJ said.

“The Philippine government should drop legal action against Rappler and allow the media in the Philippines to do its job without harassment.”

In a tweet, the Reuters Institute for the Study of Journalism at Oxford University described the move as “the latest attempt to intimidate independent journalists and silence one of the few critical news outlets left in the country”.

Martin Baron, the editor of the Washington Post, described the move as “an attack on one of the world’s bravest journalists”.

Duterte had already banned a Rappler reporter from his news briefings after the government’s corporate watchdog found that the organisation violated a constitutional prohibition on foreign ownership when it received money from an international investment firm. Rappler rejected the ruling.

Duterte has accused several independent media groups in the Philippines of biased reporting, including on coverage of his crackdown on illegal drugs that has left thousands of mostly poor urban residents dead, and drew condemnation by western governments and UN bodies.

“We are not at all surprised about the decision, considering the track record of how the government has treated Rappler as a result of its independent and fearless reporting on what has been transpiring in the country,” Rappler’s legal counsel, Francis Lim, said.

He denied the charges of tax evasion in connection with Rappler’s bond sales in 2015 to two foreign entities. Rappler, which was founded in 2012, says it remains wholly Filipino-owned and that the foreigners have no voting rights nor a say in its management and news operations.

Duterte accused Rappler last year of being US-owned, in violation of the Philippine constitution, and alleged the news outfit was funded by the CIA. Rappler denied the allegations.

In a speech on Friday after accepting an award from the International Center for Journalists in Washington DC, Ressa appealed to “the men and women who work in governments like mine using a scorched-earth policy to grow and retain power, appealing to the worst of human nature: you have the power to stop the erosion of democracy and maintain the rule of law”.

She added: “We are Rappler, and we will hold the line.”