Military spokesman Lieutenant Colonel Jo-ar Herrera said the armed forces' social media unit uncovered 63 Facebook accounts belonging to the jihadists and their supporters.
"These 63 accounts are spreading malicious information and misinformation that affect the information landscape and the mindset of every Filipino," Herrera told a news conference in the southern city of Marawi.
The military has asked Facebook Philippines "to conduct necessary measures to take down these fake accounts," Herrera said.
They have so far fended off more than two weeks of air and ground assault by government forces.
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President Rodrigo Duterte said the attack was part of a wider plot by IS to establish a base in the southern region of Mindanao, and declared martial law there to quell the threat.
Forty government troops and 138 militants, have been confirmed killed due to the fighting, according to Herrera.
Twenty civilians have also been confirmed killed but the true number is likely to be higher with authorities yet to fully assess the roughly 10 percent of Marawi still being held by the militants.
IS jihadists have made extensive use of social media to strike fear and spread their ideology, and analysts have said many of their followers were radicalised by reading and listening to online propaganda material.
When asked about the military's request, Facebook told AFP it would remove accounts that promoted terrorism.
"We want to provide a service where people feel safe. That's why we have community standards that explain what you can and cannot do on our service," a Facebook statement said.
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