The items have been kept in a storage facility next to a concrete factory and the resulting contamination meant staff were banned from entering the site for much of 2022.
"There's a build up of silica dust in the facility, which requires removal before any collection can be treated," the museum's Ruth Wilson told a senate estimates hearing late on Thursday.
In April, the federal government announced a $78.3 million funding boost for the institution over the next four years.
That included $13.1m to lease an "urgently needed" new storage facility and move the items from their current site.
The objects include machinery, agricultural equipment, boats, trucks and planes, all of which the museum regards as "relatively robust".
The institution leased the premises in 1988 when there were no other buildings nearby, but it won't reveal the location of the contaminated site.
It is not known how long the collection items have been stored next to the factory.
The storage facility was closed for several months during 2022 while independent hygienists tested dust levels.
After two rounds of testing showed silica dust levels were within acceptable limits and could be managed by staff wearing personal protective equipment, the ban on entry was lifted in early 2023.
The museum has not received any reports of damage to collection items and decontamination processes are under way, a museum spokesperson said.
The museum says the quality of the building is exacerbating the problem by letting contaminants in, an issue it raised with the building's owners in December 2022.
Dust produced from silica is linked to the incurable lung disease silicosis as well as cancer and Safe Work Australia has recommended a national ban on products using silica.
"Workplace exposure to respirable crystalline silica has led to an unacceptable increase in the number of cases of silicosis and other silica-related diseases," Safe Work Australia chief executive Michelle Baxter said in March.
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