監管機構的裁決是在杜特爾特離任並由他的盟友小費迪南德-馬科斯（Ferdinand Marcos Jr.）在5月贏得選舉之前做出的。
一位專欄作家JC Punongbayan在推特上說，該命令 "不是立即執行的"，並補充說將是 "照常營業"。
由於她在Rappler的新聞工作，她去年被授予諾貝爾和平獎--與一名俄羅斯記者一起。她因利用言論自由 "揭露她的祖國菲律賓濫用權力、使用暴力和日益增長的獨裁主義 "而受到讚揚。
The regulator's ruling comes just before Duterte leaves office and is replaced by his ally Ferdinand Marcos Jr. who won election in May.
"We are entitled to appeal this decision and will do so, especially since the proceedings were highly irregular," the news site said in a statement.
The Philippines Securities and Exchange Commission said in a statement that a decision to revoke the company's licence to operate had been upheld following an appeal - because it and the courts had concluded that Rappler's funding model was unconstitutional.
The regulator first issued an order against Rappler in 2018, invalidating the news organisation's credentials because - it said - the company had sold control of itself to a foreign entity in breach of foreign ownership restrictions in Philippines media.
In 2015 Rappler received funding by the Omiydar network - a philanthropic investment company set up by Pierre Omiydar, the billionaire founder of Ebay - but denied it ceded foreign control. Three years later it donated the investment to Filipino staff of Rappler to prove it had no controlling stake in the business.
The news site said in a statement that the latest order for now "effectively confirmed the shutdown of Rappler", but it was not clear whether this meant the site would stop publishing immediately.
One columnist JC Punongbayan tweeted the order was "not immediate and executory", adding that it would be "business as usual".
Rappler has published extensively on the President's Duterte's deadly war on drugs, as well as taking a critical look at issues of misogyny, human rights violations and corruption.
Ms Ressa, who co-founded the site in 2021, has repeatedly faced numerous legal cases which she says are politically challenged. In 2020 she was convicted of libel in a case seen as a test of Philippine press freedom.
She was awarded the Nobel Peace Prize last year - along with a Russian journalist - for her journalistic work with Rappler. She was commended for using freedom of expression to "expose abuse of power, use of violence and growing authoritarianism in her native country, the Philippines".