The country's constitution says mass-media entities must be wholly owned by Filipinos. The SEC claims that Rappler violated those rules when it received money from Omidyar Network, a fund created by eBay founder Pierre Omidyar, who is not Filipino.
Rappler denies wrongdoing and has stated publicly that Omidyar's investment was made through depository receipts that allow companies to invest in local media outlets without ceding ownership.
In a statement published Monday, the company said the decision amounted to a gag order.
"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," the statement read.
Sen. Risa Hontiveros said the decision reminded her of the era of former dictator Ferdinand Marcos.
"The revocation of Rappler's registration is pure harassment and a clear attack on press freedom," she wrote on Twitter. "It is also Marcosian. It's a move straight out of the dictator's playbook."
She added: "I urge the public and all media practitioners to defend press freedom & the right to speak truth to power."
Many Filipino journalists view the SEC case as a bid to stop Rappler's dogged and affecting reporting on Duterte's campaign against suspected drug users and dealers.
Duterte and his allies have repeatedly threatened the news outlet. In last summer's state of the nation address, for instance, he called out Rappler by name.
The Foreign Correspondents Association of the Philippines and the National Union of Journalists of the Philippines condemned the ruling, as did many prominent Filipino journalists.
Rappler said that it does not plan to stop operating and that it will pursue the case in court.
"We intend to not only contest this through all legal processes available to us, but also to fight for our freedom to do journalism and for your right to be heard through an independent platform like Rappler," the statement said.
"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."