Hayabusa, the unmanned probe fired a small metal ball on Saturday at the surface of the asteroid to stir up material for collection, and the operation was carried out "without failure," a spokesman for the Japan Aerospace Exploration Agency (JAXA) said.
More data confirming the mission's success is expected later in the day after scientists have examined additional transmissions from the probe, spokesman Kiyotaka Yashiro said.
But JAXA will not know for sure if Hayabusa collected surface samples until it returns to Earth. It is expected to land in the Australian Outback in June 2007.
If so, it would be the first time that soil samples have been taken from an asteroid, the space agency said, and could help scientists learn more about how the solar system was created.
A Nasa probe collected data for two weeks from the asteroid Eros in 2001, but did not return with samples.
"The samples could be something like fossils of the solar system"
Spokesman for the Japan Aerospace Exploration Agency
"As this asteroid was estimated to have emerged roughly 4.6 billion years ago, when the solar system was created, the samples could be something like fossils of the solar system," the Yashiro said.
The Hayabusa probe, which successfully touched down on the rotating Itokawa asteroid 290 million km from Earth last Sunday but failed to collect material, made a second attempt early on Saturday.
The mission was all the more difficult because the potato-shaped Itokawa asteroid is revolving, making it tough for Hayabusa to land on a targeted site, ideally a flat area between cliffs on the jagged surface.
Last Sunday's touch down was the first time that a space probe landed and departed from such a celestial body, but on that occasion the probe temporarily lost contact with Earth for technical reasons.
Hayabusa was launched in May 2003 with a budget of 12.7 billion yen (just over $100 million) and is scheduled to return to Earth in June 2007, after travelling a total of two billion km.