The Abbott government has had to temporarily ditch one childcare-related budget savings measure to get another through parliament.
The coalition wants to continue a pause on the childcare rebate of $7500 a child a year, as well as freeze childcare benefit income thresholds.
Labor agrees with the first measure but opposes the latter.
The changes were originally included in a single bill but the government on Monday reluctantly agreed to a Labor amendment to split them.
Human Services Minister Marise Payne said the government would reintroduce the benefit threshold changes in a separate bill "as soon as possible".
The amended bill will now head back to the lower house for the tick of approval.
Labor has accused the government of trying to rush through the benefit changes without conducting a proper assessment of the financial impact on the community.
The rebate freeze was introduced by the previous Labor in 2011. It intended to extend the freeze for another three years but never legislated to do so.
The Greens say both measures are part of the government's attack on families and the government's bill should have been voted down in its entirety.
The government has set up a productivity commission inquiry into the future of childcare and early childhood learning, with a draft report expected in July.
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