It came as the Jakarta presidential palace also prohibited playing the popular game around the premises, with signs appearing that read "Playing or hunting Pokemon is forbidden in the area of the palace".
Indonesians have joined the frenzy for Pokemon Go, which has become a worldwide hit since launching two weeks ago and has already been blamed for a wave of crimes, traffic violations and complaints in cities around the globe.
But its popularity has caused concern among the security establishment's top echelons, with officials suggesting its high-tech capabilities could be put to use in spying.
"Spying can come in different forms," said hardline Defence Minister Ryamizard Ryacudu, adding that the game was "just not right".
The military will soon issue an order banning all personnel from playing Pokemon Go during work hours as it seeks to protect high-security sites, military spokesman Tatang Sulaiman told AFP.
The announcement came after a Frenchman was briefly detained this week when he accidentally wandered onto a military base on Java island as he played Pokemon Go.
Police officers across the country were already sent an order on Tuesday banning them from playing the game while on duty, a spokesman said.
"We are worried that police officers may become addicted and we don't want that because a police officer's duty is to serve the public. The job requires hard work and concentration," said national police spokesman Boy Rafli Amar.
Pokemon Go uses smartphone satellite location, graphics and camera capabilities to overlay cartoon monsters on real-world settings, challenging players to capture and train the creatures for battles.
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