Business groups have raised concerns about the multi-employer bargaining changes, which will essentially make it easier for employees at multiple businesses to band together to call for higher wages and better conditions.
Workplace Relations Minister Tony Burke has agreed to amend the bill so businesses with smaller staff numbers are not forced into multi-employer agreements by larger groups.
"This is a reasonable concern," he told Sky News on Sunday.
The bill will be amended so a majority of staff at each employer will need to agree to take part in bargaining or any other stage in industrial relations activity.
"That puts an end to the argument that if businesses didn't want to be part of an agreement, they could still get roped in," Mr Burke said.
Mr Burke said he had been consulting with business groups about the bill in the past week, including the Council of Small Business Organisations Australia, Ai Group, the Business Council of Australia and the Australian Chamber of Commerce and Industry.
Business groups have also called for key sectors, such as mining, to be carved out of contention for multi-employer agreements.
Mr Burke said the mining industry was largely covered by enterprise agreements so were unlikely to engage in multi-employer bargaining anyway.
There have also been calls to carve out enterprises with fewer than 100 employees from multi-employer agreements. Small businesses with fewer than 15 people have already been excluded.
Mr Burke expects the minimum business size to be discussed as the bill moves through parliament but stressed it was important for all employees - no matter the size of their employer - to see their wage increasing.
"We want to want to get wages moving for everyone," he said.
Nationals leader David Littleproud said the government needed to be more transparent about the possible downsides of the proposed legislation.
"If you have the ability for more strikes, businesses will have to recalibrate and employ less people, and it will also hurt at the checkout," he told Sky News.
"The government needs to be more open and transparent."