To get at those crucial materials, an "impactor" was sacked from Hayabusa2 towards Ryugu in April, 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.
JAXA officials said they had also observed signals indicating the probe had risen from the surface as planned. "Project Manager Tsuda has declared that the 2nd touchdown was a success!"
Earlier this morning, JAXA also released a series of images taken immediately before and after the spacecraft's touchdown on Ryugu showing the gravel blasted out from beneath the surface that is now scattered across the asteroid's surface.
"We obtained pieces of the history of the solar system. We love you, take care Hayabusa2", the musician told the team.
Asteroids are rocky remnants left over from the formation of the solar system.
The brief landing Thursday is the second time Hayabusa2 has touched down on the desolate asteroid Ryugu, some 300 million kilometres (185 million miles) from Earth.
With the collection of the samples, the probe's mission is nearly complete, and it will start its journey back to Earth at the end of this year.
The spacecraft had started its gradual descent from its home location on Wednesday.
JAXA officials said earlier that the probe appeared to have landed successfully, but confirmation came only after Hayabusa2 lifted back up from the asteroid and resumed communications with the control room.
The landing is the second successful attempt to touch down on the asteroid.
"It would be safe to say that extremely attractive materials are near the crater", Hayabusa2 project manager Yuichi Tsuda said.
The landing was a challenge for Hayabusa2 because of the risk of getting hit by dust and debris remaining at the crater, Kubota said.
He said JAXA plans to send the spacecraft, which was on its way back to the home position above the asteroid, to examine the landing site from above. Initial images transmitted from Hayabusa2 show sample pieces with different colors and sizes, a sign of diversity even on a tiny asteroid, he said. "I'm so excited about finding out about all these unknowns".
Japanese space probe Hayabusa2 on Thursday made its second successful landing on an asteroid located 244 million km from Earth, collecting underground samples that could provide information on the origin of the solar system.
The second landing was about the last chance for Hayabusa 2 because surface temperatures on Ryugu were increasing as the asteroid's orbit was bringing it closer to the sun.
JAXA Research Director Takashi Kubota speaks to journalists during a press conference following the Hayabusa2 probe's touchdown on the asteroid Ryugu, at the Institute of Space and Astronautical Science (ISAS) of Japan Aerospace Exploration Agency (JAXA) in Sagamihara city, Kanagawa prefecture, July 11, 2019.