Australian National University in Canberra was forced to shut down for two days following the storms to assess the damages.
An area particularly affected by the dust cloud was the rural city of Dubbo.
Cars were dented and windows were smashed as over 1,000 homes lost power across the suburbs in the Australian Capital Territory, local media reported.
Hundreds of cars and buildings were badly damaged, and the hail penetrated 65 glasshouses at the CSIRO's Black Mountain site, ruining studies on crop sustainability.
Animals were injured during the storm, with parliament staff looking after a bloodied crow that copped a hailstone to its head. They show his country in New South Wales that was charred and smoky 10 weeks ago and fresh green on Sunday after heavy rains.
The bureau said the low-pressure system that prompted the thunderstorm warning would move east to the Tasman Sea on Monday night.
"The dust storms affecting central western New South Wales are a direct effect of two years of drought and greatly diminished vegetative cover on the soil surface", said Stephen Cattle, a soil scientist at the University of Sydney.
The rainfall that came as part of the severe weather conditions helped relieve some parts of the country affected by the bushfires, but caused damage in other ways, the BBC reported.
A total fire ban has also been declared for the North Western fire weather area in NSW.
"I'm urging people to ask themselves the questions - what would you do with your pets, your auto or loose outdoor furniture if a storm was to hit?"
The risky storms came at the end of a weekend that brought a massive dust storm to the western parts of New South Wales - another blatant turn in Australian summer with extreme weather.
The storms follows huge dust storms swallowing up large swathes of the Central West slopes and plains on Sunday afternoon.
Firefighters are working to slow the spread of fire and build containment lines while the rain lasts, with increased fire danger expected later this week.
The Canberra Times reports one researcher rushed to the site to cover their work during the storm.
Authorities there are bracing for elevated fire danger on Thursday, when temperatures in parts of the state will tip above 40 degrees Celsius (104 degrees Fahrenheit). "3mm of rain since Wednesday and two of these since Friday", said one resident, according to the Independent.