The ASTRO-H satellite, developed in collaboration between the agency, NASA and other groups, is set to orbit at an altitude of about 580 kilometres and observe X-rays emanating mainly from black holes and galaxy clusters.
The satellite was carried out by the country's mainstay H-IIA rocket, which soared towards the heavens from the Tanegashima Space Centre in southern Japan under mostly clear late afternoon skies.
The broadcast was nationally televised and the Japan Aerospace Exploration Agency said the satellite separated from the rocket with no difficulty.
The Japanese rocket, which was initially scheduled for liftoff last Friday but was postponed due to bad weather, was launched at 5:45 pm local time.