The scars are each more than 120 miles in diameter and are believed to mark the spot where a meteorite split into two, moments before it slammed into earth.
The impact is believed to have occurred more than 300 million years ago.
Scientists discovered a scar from the meteorite five years ago – it was then thought to be from the third largest crater ever found – but now say there are two sets of remains.
Dr Andrew Glikson, from the Australian National University, said the structures could have resulted from a single meteorite which split.
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The crater itself has long since disappeared but samples from the twin scars were discovered deep beneath the ground during drilling as part of geothermal research.
"The two asteroids must each have been over ten kilometres [six miles] across – it would have been curtains for many life species on the planet at the time," he said.
"Large impacts like these may have had a far more significant role in the Earth's evolution than previously thought."
Evidence of the impact zone was found more than 1.2 miles underground in the Warburton Basin, near the borders of the states of South Australia and Queensland and the Northern Territory.
Dr Glikson said the date of the impact was unclear but it probably occurred more than 300 million years ago.
"It's a mystery – we can't find an extinction event that matches these collisions," he said. "I have a suspicion the impact could be older than 300 million years."
The surrounding rocks are 300 to 600 million years old but are not accompanied by a layer of sediment which contains evidence of a mass extinction; such layers are typically found near large meteorite strikes.
The research has been published in the journal Tectonophysics.
"These are deeply buried impact structures," Dr Glikson said.
"When a large impact occurs the crater's contents are blown into the atmosphere, although relics of the crater may in some instances be preserved."
Ten largest craters previously found on Earth
100 miles diameter
South-West of Johannesburg, the Vredefort Dome was created over 2,000 million years ago when a meteorite struck earth. It is the oldest crater made by either a meteorite or a comet and it is reportedly the site of the largest energy release in the world’s history.
The multiple-ringed Vredefort Crater in South Africa (Nasa)
The Chicxulub crater is buried beneath Mexico’s Yucatan Peninsula. It was created by an asteroid and its impact is expected to have caused earthquakes, megatsunami, global firestorms and aerosol clouds. Many scientists believe it played a major role in the “KT Extinction Event” which caused dinosaurs to become extinct.
Remnants of the Chicxulub impact crater (Getty)
Scientists have debated whether the Sudbury crater was caused by a comet or an asteroid. Research published at the tail-end of last year suggests it was a comet – comets are made predominantly of ice, whereas asteroids are made of rock. Created 1.8 million years ago, the crater is now a valuable source of gold, copper, nickel, palladium and other metals.
Sudbury Basin in Canada (Alamy)
The Popigai crater sits in northern Siberia. It was created by an asteroid and the impact was powerful enough to send debris flying into other continents. In the 1970s, the USSR discovered the crater contained trillions of carats of “impact diamonds” - used for industry and science.
The Popigai crater in Russia (www.passc.net)
Nearly 600 million years ago, an asteroid hit what is now South Australia. Over time, the crater has been eroded but Lake Acraman, a dry lake, marks its location.
Lake Acraman, a small, shallow salt lake in the arid Australian outback (Nasa)
Quebec’s Lake Manicouagan is a remnant of one of the largest impact craters still preserved on the earth’s surface. Scientists believe it was created by a 5-km-wide asteroid over 200 million years ago. Today, the lake serves as a reservoir and it is an important spot for salmon fishing.
Hidden beneath the Kalahari Desert is the Morokweng crater. It was formed by an asteroid, which is estimated to have been between 5 and 10km wide. In 2006 scientists drilling in the area discovered a beachball-sized fossil meteorite which had survived the collision.
The heavily eroded Kara crater has been linked to the nearby Ust-Kara crater. There is dispute whether the two craters were formed separately or if they were formed in a single impact event. If they were considered together, they would form one of the largest craters on earth of 120km.
The Beaverhead crater spans central Idaho and western Montana. It is estimated to be 600 million years old. Although the crater has become weathered, there are geological features such as shatter cones and shocked rocks.
Australia has over 30 impact craters discovered so far. Located in Queensland, Tookoonooka was discovered in the 1980s when the area was undergoing petroleum exploration.