A H-IIA rocket blasted off at 9:17am (0017 GMT) today from the Tanegashima space centre in southern Japan carrying the "Michibiki" No.2 satellite, footage by Japan Aerospace Exploration Agency showed.
Satellite geolocation systems, initially designed for the US military, now power countless civilian applications, from car navigation to internet browsing on mobile phones.
Japan aims to build its version with four satellites focusing on the country and wider region.
The first satellite was put into orbit in 2010 and the third and fourth are to be launched by March 2018 to start the service.
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Michibiki, meaning guidance in Japanese, is intended for civilian use, with a claimed positioning accuracy down to mere centimetres (inches).
Though GPS is widely used in Japan, having supplementary satellites is important in a country where mountainous terrain and high buildings may interfere with GPS signals.
Japan aims to establish a constellation of seven satellites by around 2023.