Ministers are concerned that not enough schools are using super-assistants, who are allowed to take classes without a teacher present.
Higher level teaching assistants (HLTAs) are a key plank in the Government's drive to "personalise" education by helping teachers tailor lessons to pupils' individual needs. But the latest figures show that only around 14,500 of England's 153,100 teaching assistants have qualified for the status.
And union officials estimate that just one in 10 higher-level assistants are being used in the role full-time and being paid for it.
Some employers are exploiting the status to move nursery nurses on to cheaper contracts.
Jim Knight, schools minister, told local authority leaders this month: "The priority for us at the moment in respect of the workforce is support staff, and I don't think we can do this next stage (of school reform) without remodelling. The numbers of higher level teaching assistants being used are pretty limited and we would like to see that develop."
Unison, the largest support staff union, said the reforms were being undermined by schools paying higher-level rates only for the specific hours when assistants undertake higher-level duties, such as teaching whole classes.
Last year The TES revealed that some were being paid as little as an extra 15p an hour for this work. Christina McAnea, Unison head of education, said only a fraction of staff with higher-level status were being paid to do the role and only for a couple of hours a week.
"It is making people think 'Why am I bothering to do this if I only get, say, pound;10 a week extra?'" she said. "It is completely undermining what was supposed to be a career structure for support staff."
Meanwhile nursery nurses, who enjoy year-round contracts, are being asked by some employers to convert to higher-level status so they can be paid only during term-time and for fewer hours in the school week.
One nursery nurse at a primary in the north west said she had lost nearly pound;140 a month after being asked to choose between redundancy and higher-level status.
She is now teaching a core subject to reception pupils three days a week, even though she has not trained as a teacher.
"They are gradually bringing in HLTAs. It's cheap labour," she said. "If I had a child in reception and they had a nursery nurse teaching them, I would not be very happy."
Ms McAnea said she knew of several other authorities where this tactic was being used.
There are 287,500 school support staff (or their full-time equivalent) in England.
153,100 are teaching assistants.
14,500 are higher level teaching assistants.