The Protecting Your Super Package forms part of the 2018/19 Budget, which was released on Tuesday.
Data shows that there were around 9.5 million super accounts with balances of less than A$6,000 (£3,310, $4,482, €3,771) in 2015/16.
The changes are aimed at preventing the application of hundreds of millions of dollars in fees on these accounts, O’Dwyer said.
The government will also ban exit fees for all superannuation accounts, which were estimated to cost around A$37m in 2015/16.
“The ban is a significant win for the many Australians who want to rollover their accounts to a different fund, or who hold multiple accounts and see exit fees as a barrier to consolidating their accounts,” she added.