Childcare centres have been told they can no longer operate school-run services unless they have a PSV (public service vehicle) licence.
Some creches and nurseries have subsequently had to set up accounts with taxi companies.
John Fleck from Hillcrest nursery in Belfast said childcare was "already dear enough".
Department of the Environment officials have agreed to meet childcare representatives over the issue.
"Places have just been re-rated commercially and we've now had bills in for water rates," said Mr Fleck.
"We have to pass all this on to the parents, and now they're asking us to pass on taxi fares."
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