The University of the Philippines first identified the accounts over the weekend following the protest on its campus on Thursday. Those spotted carried names of students who were among eight people arrested during the protest.
Dozens of Facebook users have since posted screenshots of accounts using their names and urged friends to report the duplicates.
Justice Secretary Menardo Guevarra said he has ordered the cyber crime office and National Bureau of Investigation to “get to the bottom of this huge anomaly”.
A Facebook Inc spokesperson said the U.S. firm was investigating reports of “suspicious activity” and would act on accounts violating its policies.
Filipinos spend more time on social media than any other nationality, according to a recent study. Platforms such as Facebook have become political battlegrounds, with so-called influencers emerging as a force behind President Rodrigo Duterte’s 2016 election campaign and defending him ever since.
Opposition Senator Francis Pangilinan said he suspected the accounts targeted those who oppose Duterte’s anti-terror bill.
A presidential spokesman previously said the bill is patterned on those used in countries that had dealt effectively with extremism. Critics have said the bill could give the president unprecedented power to target them.
“We just need to stand together against possible tactics seeking to silence our voice,” the student representative of the state-funded university said in a statement opposing the accounts.
Raymund Liboro, head of the National Privacy Commission, said it was too early to draw conclusions on the motivation for the accounts. He told Reuters he had been informed by Facebook that the company had taken many of them down.
Facebook in May said it estimated the prevalence of fake accounts among its worldwide monthly active users at 5%.