The blast-off of Hayabusa2 was now pushed back by two days to 0422 GMT on Wednesday, the Japan Aerospace Exploration Agency (JAXA) said.
The agency said it decided on the second postponement due to fears of strong winds, and warned that the launch could be delayed further depending on the weather.
JAXA had originally planned to launch Hayabusa2 on Sunday, but delayed it to Monday due to a forecast of thick cloud and then announced the latest postponement.
The USD 260 million project will send the explorer towards the 1999JU3 asteroid in deep space.
Also Read
It will blast a crater in the asteroid to collect materials unexposed to millennia of wind and radiation, in the hope of answering some fundamental questions about life and the universe.
Hayabusa2 will take off only weeks after a European spacecraft's historic landing on a comet captivated the world's attention.
It is expected to reach the asteroid in mid-2018 and spend around 18 months near it.