Duterte's tirade against Rappler is ironic considering that his government is pursuing constitutional reforms that would allow foreign ownership and control of the media.
Two years into Dutetre's presidency, press freedom in the Philippines is now facing its greatest existential challenge since the downfall of the Marcos dictatorship.
"You are not only throwing toilet paper, you are throwing shit at us", the 72-year-old leader said.
Hheli Kiline, the HRW Asia deputy chief, warned of a "chilling effect if President Rodrigo "Rody" Duterte would "succeed in silencing Rappler".
Rappler said its filings to the SEC in 2015 made it clear that foreigners had invested in some of its Philippine Depositary Receipts (PDRs), but did not own any shares.
Rappler has rejected the ownership allegations, saying its foreign investors are not the owners.
The news outfit said the SEC decision amounted to "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".
The presidential palace said the SEC decision was not an attack on press freedom.
"If the president wanted to do that, he could have just sent the armed forces to their offices and padlocked them, which has been done by other regimes".
In an order, Aguirre said the NBI, "through Director Dante A. Gierran, is hereby directed and granted authority to conduct investigation and case buildup over possible violations of the Constitution and laws".
He said the PDR was made as part of "an elaborate scheme to circumvent the constitutional prohibition on foreign ownership".
"Before you criticize others, look into the mirror".
SEC Secretary Armando Pan said the January 11 decision announced on Monday was, however, "not final and executory", and Rappler "may continue" to operate pending appeal.
With this provision, foreigners holding Rappler PDRs have some kind of say in its running.
The Philippine Securities and Exchange Commission said Rappler violated Philippine constitutional restrictions on mass media ownership, which require that media properties be locally owned and operated, by receiving funding from Omidyar Network, a USA -based philanthropic investment firm, news reports said.
Next go read the SEC ruling.
Rappler CEO Ressa, in a press conference shown live on Facebook, said the SEC decision was political in nature. Rappler will continue to operate while it is appealing the decision.
Duterte also hit out anew at the former owners of the Philippine Daily Inquirer, another media outlet known for scrutinising his government, accusing them of being oligarchs who evaded tax.
Amnesty International called it "an alarming attempt to silence independent journalism", describing Rappler as "fearless in holding those in power to account".
The mass media watchdog group National Union of Journalists of the Philippines also slammed the government's decision.
The President asked where media's sense of values is, and if Rappler does not feel ashamed that it is being funded by foreign money. "The pattern suggests a policy of assaulting and weakening the press as an institution".
PRESIDENT Duterte yesterday lashed out at online media news outlet Rappler, calling it a "fake news outlet".
Rappler, emerging as an influential news source in the Philippines, hosted him at a 2016 forum for presidential candidates called #TheLeaderIWant. All three have been closely reporting on his government's drug war.
Historically, the Philippine media have been considered the freest and liveliest in Asia.