In February, the Coalition introduced a so-called omnibus bill to try to force nearly $4 billion in savings through the Parliament.
The bill included increases to childcare subsidies, bundled in with cuts to family tax benefits and paid parental leave.
The changes to the childcare system appear likely to be blocked in the Senate, because key crossbenchers are concerned they come at the expense of other cuts.
Education Minister Simon Birmingham has released data showing there was a 7.6 per cent increase in childcare fees in the June quarter of 2016, putting added pressure on family budgets.
"Australian families and taxpayers are wearing a heavy burden because of incessant fee increases across the childcare sector, and it's further evidence why the Turnbull Government's comprehensive reforms to the childcare sector are so necessary," Senator Birmingham said.
Senator Birmingham has already argued that many families have already reached the childcare subsidy cap for this financial year.
But he would not be drawn on whether the Coalition would be prepared to split the bill to at least get some of the savings measures over the line to pay for the childcare changes.
"The Turnbull Government still expects the Parliament to support our savings measures that are necessary to pay for increased investment in child care," he said.
"We're continually talking and speaking with the crossbenchers in the Senate to see if there are pathways to pay for our childcare reforms, and to get them enacted.
"What we'd really like to see is the Labor Party come to the table and ensure that we can get these savings passed, to enable childcare reform to happen.
"I'm not in the business of speculating about how negotiations are progressing, but we absolutely want to see our childcare reforms pass the Parliament during these next two weeks of sittings, so that we can give certainty to families and to childcare providers that help is on the way."
Labor has also said it supported the changes to childcare subsidies, but not at the expense of family welfare cuts.
"If Malcolm Turnbull wants to deliver childcare assistance to Australian families, we will do it tomorrow if he listens to Labor's suggestions and drops his cruel cuts," Opposition child care spokeswoman Kate Ellis said.
"We don't believe that you need to hit 1.6 million Australian families with cruel cuts in order to deliver on childcare reforms which have been promised for years.
"The Government has many options. This is about priorities."