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Civil servant Alexander Aan, 31, is now in protective police custody after he was attacked by an angry mob earlier this week.
He may also lose his job over his posting on the social networking site.
Atheism is a violation of Indonesian law under the founding principles of the country.
Indonesia - the world's most populous Muslim nation - recognises the right to practice five other religions aside from Islam, says the BBC's Karishma Vaswani in Jakarta.
Local media said a mob attacked Mr Aan when he arrived for work at a government office on Wednesday.
Police said that according to Indonesian criminal law, anyone who tried to stop others believing in a faith could face up to five years in prison
The Facebook page where he made his comments is now unavailable. Supporters of Mr An have urged police to release him.
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