The Muses-C space probe is scheduled to visit the 1998 SF36 asteroid, 300 million kilometres (186 million miles) from Earth, and bring back rock samples.
These samples should help scientists understand how the Solar System was formed.
"Asteroids are known as the fossils of the Solar System," said mission leader Junichiro Kawaguchi, of Japan's Institute of Space and Astronautical Science.
"By examining them, you can find out what substances made up the Solar System, including Earth, in the distant past."
The probe was launched on Friday on top of a $60m (7bn yen) M-5 rocket from the Kagoshima Space Centre on the southern Japan island of Kyushu.
Muses-C will spend about five months near the asteroid, one of the nearest to Earth, making observations of its surface and gathering samples.
Rugby ball
To collect samples, the probe will make three brief touch-and-go contacts with 1998 SF36, each time firing a small projectile into its crust.
The probe will then scoop up the resulting rock fragments in a cone-shaped funnel.
Even a tiny amount of matter from the asteroid, which is 500 metres long and shaped like a rugby ball, will be sufficient for research purposes.
When the probe returns to Earth, which is expected to be in the summer of 2007, the sample container is designed to break away and parachute back to land in the Australian desert.
If successful, Muses-C will be the first probe to make a two-way trip to an asteroid.
A United States Nasa probe collected data for two weeks from the surface of the asteroid Eros in 2001, but did not return with samples - although it did become the first spacecraft to successfully land on an asteroid.
The latest lift-off follows another Japanese rocket launch in March, when the H-2A rocket, Japan's main launch vehicle, put the country's first spy satellites into orbit.
Japan hopes the H-2A will one day compete in the commercial satellite launching business.
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