The country's Security and Exchange Commission (SEC) said
online news site Rappler had violated the country's constitution and its registration would be revoked over foreign ownership rules.
The outlet has been fiercely critical of president Rodrigo Duterte's administration since the controversial leader came to power in June 2016.
Rappler's founder and CEO, Maria Ressa, told CNN the organization plans to fight the decision.
"We plan to take this to the next legal remedy, to the next court, all the way up to the supreme court," Ressa, who is a former CNN employee, said.
In a statement Monday, Rappler said the move was unprecedented and it would continue to operate despite the order to close shop.
"We will continue bringing you the news, holding the powerful to account for their actions and decisions, calling attention to government lapses that further disempower the disadvantaged," the editorial statement
"The SEC's kill order revoking Rappler's license to operate is the first of its kind in history -- both for the (SEC) and for Philippine media," the statement reads.
"What this means for you, and for us, is that the Commission is ordering us to close shop, to cease telling you stories, to stop speaking truth to power, and to let go of everything that we have built -- and created -- with you since 2012."
On Tuesday, Rappler reported
that the SEC had said the company could continue to operate until it exhausts legal options.
Presidential spokesman Harry Roque told CNN affiliate CNN Philippines
Monday that the office of the president had "nothing to do with the SEC decision."
Central to the revocation, the SEC says, are questions surrounding Rappler's ownership.
Constitutionally, mass media companies in the Philippines are blocked from foreign ownership, and the SEC alleges that Rappler's parent company "intentionally created an elaborate scheme" to cover an investment from a foreign source, and that the media organization is a "mass media entity that sold control to foreigners."
The investment in question comes from the Omidyar Network,
a investment vehicle created by eBay founder and entrepreneur Pierre Omidyar, Rappler said.
The Omidyar Network "invests in entrepreneurs who share our commitment to advancing social good," an introductory page on its website says.
Rappler denies foreign ownership, and says the Philippine Depositary Receipt (PDR), a financial instrument that governs the Omidyar investment, doesn't give the Network any control over the company. It says the arrangement was accepted by the SEC in 2015.
In his State of the Union address in 2017, Duterte singled out the company, criticizing its ownership structure and claiming it was "fully owned by Americans."
In a report on the speech
at the time, Rappler contended that it was "100-percent owned by Filipinos."
The Office of the Solicitor General (OSG) welcomed the decision, according to CNN Philippines.
"This decision demonstrates that even influential media outfits cannot skirt the restrictions set forth in the Constitution. Rappler is free to seek redress before our courts," Solicitor-General Jose Calida said.
"The OSG is ready to defend the sound decision of the SEC in any forum."
Journalists, rights groups react
International and local groups have condemned the decision, with the Committee to Protect Journalists (CPJ) calling it a "direct assault on freedom of the press," and rights group Amnesty International saying it was "an alarming attempt to silence independent journalism."
The National Union of Journalists of the Philippines released a statement saying it was "outraged" at the decision.
It declared its "full support" for the under-fire news organization and said Duterte's annual address was "but one of many threats Duterte has made against media critical of him and his governance, such as the Philippine Daily Inquirer and broadcast network ABS-CBN, whose franchise renewal he threatened to block," referring to two other outlets that Duterte has previously criticized.
Altermidya, a nationwide network of alternative media outfits, said it was a "serious danger to press freedom and freedom of expression," and said the move "could only be interpreted as part of a scheme to silence critical media and to instill fear among media practitioners committed to reporting the truth."
Human Rights Watch alleged that it was the president who was attempting to stifle Rappler, and issued a warning for the free press in the country.
"If Duterte succeeds in silencing Rappler, it will have a profound chilling effect on Philippine media freedom, encouraging self-censorship by reporters and media outlets fearful of government reprisals for critical reporting at a time when the watchdog role of a free press is more urgently needed than ever," its statement said.
Veteran Philippines journalist Charie Villa said political reporting in the country was "an open field" and that "people with political agendas can get bashed." She called for Rappler to be completely transparent about its ownership issues.
"In the Philippines, media ownership is an issue. Generally, media owners have business interests and agenda that often clash or attached to a political party -- that's why the public ... view their content with suspicion."