A Therapeutic Goods Administration spokeswoman said one child lost consciousness and the other experienced somnolence, or sleepiness.
One case occurred in 2009 and the other in 2010, the spokeswoman said.
Cases of accidental exposure to fentanyl patches in children aged under five have also been made to the NSW Poisons Information Centre.
Sarah Spagnardi, from NPS MedicineWise, said the patches were dangerous if put in the mouth or if accidentally attached to a child's skin.
"Also, the risk of a partially detached patch being transferred from an adult to an infant is high, if young children are held by adults or sleep near each other," she said.
Ms Spagnardi said patches should be disposed carefully by folding it inwards on itself and wrapping it in paper or plastic.
- AAP