Unison says the role of assistants has increased in recent years but they have different pay and conditions depending where they work, unlike teachers.
There are claims some are qualified at a more senior level but paid at a lower grade.
The Welsh government said it does not have the power to set conditions.
But Unison says ministers could use their law-making powers and specifically the Education (Wales) Bill to standardise conditions.
Where teachers are paid over 52 weeks of the year, teaching assistants are only paid in term time.
Their salaries can also vary as pay is set by each of Wales' 22 local authorities unlike a nationally-agreed rate like teachers.
Jessica Cromie, the Unison schools lead for Wales, says the inconsistency of what was expected from different grades of support staff "exposes a deep unfairness of the way support staff are treated".
She says although the issue of assistants' conditions is not devolved, the Welsh government's Education (Wales) Bill could help as it was currently looking to improve standards across the school workforce.
"What they could do as an interim measure even if they weren't going to look at pay and conditions is they could look at this issue of role inconsistency," she told BBC Radio Wales.
She claimed some staff qualified to work at a senior level were employed on split contracts across the week - and paid to work at both the lower and top grades although they were using the same skills across the week.
Amanda Thomas, a lecturer in early years education at the University of South Wales, says in the past she taught college students looking to become teaching assistants.
She found some being used to cover work above their grade, probably because they were about £100 a day cheaper than a supply teacher.
Ms Thomas also said she knows of newly qualified teachers unable to find work as supply teachers which she believes is due to schools using teaching assistants.
Local government consultant Jeff Jones, a former leader of Bridgend County Borough Council, said with councils could only do so much as they are looking to make further austerity budget cuts in the years to come.
"If you give more money to classroom assistants it means less money for other people," said Mr Jones, a former education spokesperson for the Welsh Local Government Association which acts for all councils.
Simon Thomas, education spokesman for Plaid Cymru, said teaching assistants had become "essential" and suggested devolving pay of teachers to Wales to enable a national package to be put together to manage the terms of all education workers.
In a statement, the Welsh government said: "We do not have the power to act with regards to pay and conditions of support staff.
"Where we do have responsibilities for support staff we are working hard to help them with their training and development to deliver a highly skilled school workforce through the support staff action plan.
"We want to raise standards of teaching and leaning by ensuring learning support workers are appropriately qualified and skilled.
"The Education (Wales) Bill creates the framework to enable us to start to address this."

It will be the 30-year-old's first competition of 2016 as she prepares to defend her Olympic title in Brazil.
The double world champion missed the indoor season with an Achilles injury.
Ennis-Hill is not yet ready for a full heptathlon and will miss an event in Gotzis, Austria on 28 May.
A union has called for 17,000 teaching assistants in Wales to have a national structure for pay and conditions to end unfairness.
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Olympic heptathlon champion Jessica Ennis-Hill will begin the build-up to Rio 2016 by competing in the javelin at the Loughborough International Athletics match on Sunday.