Some nursery nurses are being left behind because they do not have the literacy and numeracy qualifications needed to qualify for higher-level teaching assistant (HLTA) status.
But teaching assistants at all levels who have taken on more responsibilities feel disillusioned about the absence of a recognised pay structure, according to the Association of Teachers and Lecturers (ATL).
HLTAs were introduced to help deliver the workload agreement, and are trained to provide cover for teachers taking their half-day-a-week planning, preparation and assessment time.
However, many nursery nurses do not have the maths andor English GCSEs (A*-C) needed to progress to higher-level status because it was not a requirement of the National Nursery Examining Board (NNEB) diploma.
Nursery nurses can take additional literacy and numeracy skills tests, but these are not funded. Colin Skinner, headteacher at Roath Park primary, Cardiff, is paying around pound;130 for two nursery nurses to take the tests.
"With all the changes to support staff, people with the NNEB qualification are being left behind," he said. "There are hundreds of NNEBs in Wales who do not have this qualification, and their years of experience count for nothing."
Paul Elliott, Unison's head of local government in Wales, said nursery nurses were in a vulnerable position because their terms and conditions were different to those of other support staff.
"We would expect schools and local education authorities to support these nurses by helping them to get the appropriate qualifications," added Mr Elliott.
But many teaching assistants who have taken on greater responsibilities since the introduction of the workload agreement feel demotivated by low rates of pay.
Last year English Education Secretary Ruth Kelly suggested the introduction of a national pay scale for support staff to reflect these increased roles, but the decision still lies with LEAs and individual schools.
According to the ATL, many pay HLTAs on an hourly basis only for their enhanced duties, and on their current rate of pay at other times. The contracts are usually term-time only. Dr Philip Dixon, director of ATL Cymru, accused schools of "penny-pinching exploitation" of dedicated staff.
He added: "We don't have to wait for Ruth Kelly to introduce a national pay scale in Wales."
Marjorie Barnes, a teaching assistant at a secondary school in north Wales, took on extra responsibilities as a cover assistant but only received an extra pound;25 a week, which she equates to pound;1 an hour if she covers five lessons a day.
"We're taking on more responsibilities but for nothing. We want a national, structured pay scale."
According to government figures, 102 assistants in Wales have met the HLTA standard, with 250 more expected to have done so by the summer. But the Assembly government does not know how many of these are actually working as HLTAs in schools, and does not fund training. England had 8,600 training places last year.
Education, lifelong learning and skills minister Jane Davidson said: "It is quite right that people working to support the work of pupils can demonstrate a good basic standard of education."
She added that any changes in pay and conditions would need to be consulted on with local authorities, the Welsh Local Government Association and unions.