As one of her last acts as Assistant Education Minister, Sussan Ley announced a crackdown on family day care workers who swap their own children between centres to rort taxpayer-funded childcare subsidies.

The changes were to come into force on Tuesday but have been postponed after concerns were raised by government MPs, independent senator Nick Xenophon and the family day care sector.

The delay is one of Mr Morrison's first official acts since being signed in as minister.

"This measure, referred to as the 'child-swapping' rule, was aimed at stamping out serious non-compliance that had arisen as a result of a number of unscrupulous family day care providers," Mr Morrison said.

"While I remain absolutely committed to stamping out these 'child-swapping' rorts, we need to ensure that we mitigate against any unintended consequences for legitimate operators and the families who depend upon them."

In one example presented to Mr Morrison, a family day care educator with a three-year-old son with disabilities would have lost access to child care subsidies because he was cared for by another educator.

Senator Xenophon said he supported cracking down on rorters but the proposed changes were a blunt instrument that could have punished legitimate educators.

"Scott Morrison listened and he acted decisively to stop thousands of family day care educators and their children being affected by these changes," Senator Xenophon said.

"There are other people in the government who could learn from his approach."

Family Day Care Australia chief executive Carla Northam said the sector "applauded" Mr Morrison for his decision and looked forward to working with him on a resolution.