A photo of the crater taken by Hayabusa2's camera after the April blast showed that parts of the asteroid's surface are covered with materials that are "obviously different" from the rest of the surface, mission manager Makoto Yoshikawa told reporters before the latest touchdown.
The probe made a brief touchdown on the asteroid around 0120 GMT, according to information received at the mission control centre, the Japan Aerospace Exploration Agency (JAXA) said.
The asteroid is about 250 million kilometers away from Earth and the successful mission is said to be of considerable scientific and strategic significance.
"We have obtained a piece of the solar system's history", said Hayabusa2's project manager Yuichi Tsuda at a press conference, adding the collection of both surface and subsurface samples would allow for their comparison.
Thursday's mission was to land inside that crater to collect scattered samples that scientists believe contain more valuable clues to the origin of the solar system.
To get at those crucial materials, in April an "impactor" was sacked from Hayabusa2 towards Ryugu in a risky process that created a crater on the asteroid's surface and stirred up material that had not previously been exposed to the atmosphere.
"Everything went perfectly, even better than ideal, as if Hayabusa were reading our minds", he said. Asteroids are building materials leftover from the formation of the Solar System. The probe is scheduled to return to Earth with its samples in 2020.More news: Ezri Konsa: Aston Villa close to signing Brentford defender
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By 10:00 a.m. on Thursday, the probe was about 30 meters above the asteroid.
Japan's Hayabusa2 has achieved another major success in its bid to return samples of an asteroid's interior to Earth. They were confident that a second landing could be pulled off. It extended its sampling tube to the ground, shot a pinball-size bullet to break open the surface, and sucked up the debris that was blasted off.
The touchdown marked the second time the spacecraft has captured rocks and dust from the surface of Ryugu, a potentially hazardous asteroid in the Apollo group.
"It would be safe to say that extremely attractive materials are near the crater", Tsuda said before the landing.
Hayabusa-2 started its mission to Ryugu in 2014, launching from Japan's space port Tanegashima, a small island located south of Kyushu Island, Japan's southernmost main island.
But JAXA scientists learned from that first mission and conducted numerous simulations using the successor probe.
"It is extremely significant to be able to compare soil on the surface and from underground", Watanabe said.