Defence Ministry spokesman David Lo said today that Apple should follow its rival Google in using only low-resolution satellite pictures to show sensitive facilities.
He acknowledged the military should also try to camouflage them.
The 10-storey high radar installation built with U.S. technology is expected to go online later this year. It's near the Hsinchu Airbase in northern Taiwan.
The satellite picture that can be viewed with iPhones is believed to have been taken a year ago.
Local media say the radar installation can monitor targets, determine their speeds and fire missiles to intercept them.