If the capsule does contain even tiny samples from the asteroid, scientists hope they will reveal important clues into the creation of the solar system.
On Monday scientists from the Japanese space agency JAXA said they had located the capsule's landing site and hoped to collect it by helicopter.
Aboriginal tribespeople will assist in the recovery of the capsule to ensure that no damage is done to sites sacred to their culture.
"The plan is to pick it up today, package it up and get it over to Tokyo as quickly as possible," Trevor Ireland, a scientist with the Australian National University, told the AFP news agency from the Woomera landing zone.
|Hayabusa sent back detailed images of the surface of Itokawa [JAXA]
He said the capsule signalling systems had activated properly and would enable scientists to track it down.
Ireland, who expects to be among the scientists who will analyse the contents of the capsule, said the landing was a "once in a lifetime" opportunity for scientists.
The capsule's return brings an end to a seven year journey that had been plagued by mishaps over its five billion-kilometre journey to the far-flung asteroid.
Hayabusa had originally been due to return to Earth in 2007 but a series of glitches including a deterioration of its ion engines, broken control wheels, and malfunctioning batteries forced it to miss its window to return into Earth's orbit until this year.
During its encounter with the 500-metre long asteroid in September 2005, the spacecraft made two touchdowns, sending back astonishing images of Itokawa's rocky terrain.
But a system designed to gather large samples from the surface failed to operate correctly.
Despite that failure scientists are optimistic that tiny particles thrown up from the asteroid's surface during the spacecraft's landing will have collected in the capsule.
Even the smallest particles weighing fractions of a gram have the potential for many years of study.
Any material the capsule does contain could shed light on the early history of the solar system, the formation of planets, and help reduce the threat of asteroid collisions in the future, scientists say.