"We confirmed the touchdown", JAXA spokeswoman Chisato Ikuta told AFP.
Ms Ikuta said the control centre had "received data that shows that the probe is working normally and is healthy".
The probe is scheduled to touchdown on the asteroid on Friday morning and begin collecting rock samples from Ryugu's surface, JAXA said, adding that if any abnormalities were detected in the landing procedure, the mission would be immediately aborted.
"I expect this will lead to a leap, or new discoveries, in planetary science", he said. If successful, the spacecraft will mine the asteroid for any information on the formation of the solar system.
Hayabusa2 is scheduled to leave Ryugu in December 2019 and to be back home a year later.
Hayabusa-2 completed its landing late on Thursday night on to the surface of the asteroid and has since fired a bullet at the rock's surface.
Scientists hope those samples may provide answers to some fundamental questions about life and the universe, including whether elements from space helped give rise to life on Earth.
The scientists are aiming to land the probe on a far smaller landing area than originally planned that is now just 6 meters in diameter.
The landing of spacecraft Hayabusa2 on the asteroid Ryugu - which is just 900 metres in diameter - came after an initial attempt in October was delayed because it was hard to pick a landing spot on the asteroid's rocky surface.
Hayabusa-2 will continue to work on the asteroid before theme comes to return to Earth.