The federal government will provide $1 million following the deadly quakes, which struck the Nangarhar and Kunar provinces, this week.
The funds will be directed through the Afghanistan Humanitarian Fund, led by the United Nations Office for the Co-ordination of Humanitarian Affairs.
"Australia works with established partners such as UN OCHA to ensure our support helps those in need, and not the Taliban regime," Foreign Minister Penny Wong and International Development Minister Anne Aly said in a joint statement on Thursday.
"Our thoughts are with the victims of this tragic earthquake, their families and loved ones, and the Afghanistan community in Australia."
The quakes also injured more than 3100 people and destroyed more than 5400 homes, the Taliban administration said.
The death toll is expected to rise, as more victims are found under rubble.
Afghanistan is trying to support survivors by providing food, shelter and medical supplies.
The first earthquake of magnitude 6.0, one of Afghanistan's worst in recent years, caused widespread damage and destruction when it struck the provinces on Monday (AEST) at a shallow depth of 10km.
A second quake of magnitude 5.5 caused panic and hampered rescue efforts as it sent rocks sliding down mountains and cut off roads to villages in remote areas.
(with Reuters)
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