Sally Holland said she was disappointed with Alun Davies' rejection of her call for a United Nations children's rights convention to be built into a bill on additional learning needs (ALN).
Mr Davies called the idea "slavish".
The Welsh Government said the bill had children's rights at its foundation.
Welsh ministers are duty bound under existing law to pay "due regard" to the United Nations Convention on the Rights of the Child (UNCRC) in making decisions.
The convention states the best interests of a child must be a top priority in all decisions.
Prof Holland wants the duty extended to staff that will implement proposals in the bill, which shakes-up how children with ALN are treated in the education system.
At a meeting of children's committee in March, lifelong learning minister Mr Davies said it had been clear to him that once the duty was placed on ministers "we will not have to go through this process of slavishly placing the same duty into every piece of legislation subsequent to it".
In a letter to First Minister Carwyn Jones, Prof Holland said it was "most disappointing" to hear Mr Davies reject her proposal for the ALN bill, which is going through the assembly.
"The minister was factually inaccurate to suggest that placing a duty of due regard to the UNCRC on those exercising functions under the... bill would be repeating the same duty that is upon Welsh ministers", wrote Prof Holland.
"It is in my view that there would be nothing 'slavish' if every piece of Welsh legislation related to children and young people had such an overarching duty enshrined within it."
Prof Holland said implementing her proposal would send "a strong message to children and their families that Wales has this commitment to internationally agreed standards on what children need in order to live fulfilled lives".
A Welsh Government spokesman said: "Our commitment to the principles of the United Nations Convention on the Rights of the Child remains absolute and the ALN bill is a demonstration of this commitment in practice."
He added that Mr Jones would respond to the points made by Prof Holland.
A minister has been accused of giving "factually inaccurate" evidence to an assembly committee by the children's commissioner for Wales.