The popular messaging apps have closed the hole that left users' accounts open to being taken over by hackers.
Encryption used by WhatsApp, Telegram and Signal is useless if devices are infected by spy tools.
Facebook has until January 31 to respond, and could be fined 1% of its turnover if found guilty of charges.
WhatsApp is seeking to push Skype and FaceTime into the shadows with the new function.
A judge ordered WhatsApp cut off on Monday for 72 hours. The reason was not made public.
WhatsApp introduces end-to-end encryption to protect users from hackers and “oppressive regimes."
Indonesia has already requested Japan's Line messaging service to block LGBT characters.
Around 42 billion daily messages are sent by the messenger app.
The popular, Facebook-owned messaging app is valued at around $19 billion.