Wages for many of the new breed of "higher level" teaching assistants (HLTAs) are only increased for the time spent on classroom cover - in effect putting them on two contracts.
Assistants are seen as vital to the Government's workforce deal, which gives teachers half a day a week outside the classroom for planning, preparation and assessment (PPA) time.
At present, teaching assistants earn between pound;7 and pound;9 an hour on average, marginally more than a cleaner but less than a call-centre worker. More than 4,000 HLTAs are expected to be trained by the end of this term, supposedly placing them on a higher rate of pay. A further 10,000 have registered to take the qualification.
But Unison, the country's biggest support-staff union, said thousands of schools are preparing to exploit the newly-trained staff by paying the improved rate - often just pound;3.50 an hour more than other assistants - only for time spent standing in front of classes.
The issue will be a flashpoint at Unison's annual local government conference in Glasgow next week, when delegates will push for new national pay scales to eradicate inequalities.
Christina McAnea, the union's head of education, said: "HLTAs are trained in 31 different roles - standing in front of a class is only one of them.
It is completely unacceptable if schools are only prepared to pay at the higher rate for one or two hours a week. Where this is happening, Unison's advice is to boycott the HLTA role."
This week, The TES learnt that the practice is widespread in local authorities including Greenwich, Essex and Darlington.
Unison delegates in the West Midlands will tell the conference that the role of HLTAs is being "undermined by employers not applying the grade throughout the working week. Members are finding themselves with two contracts."
The findings follow a TES survey of 545 schools last week which revealed most will not be able to pay for the cover needed to provide staff with a half-day for PPA time. One head of an Essex junior school said: "The bottom line is, I cannot afford to pay assistants any more than the bare minimum because of budget pressures."
Ms McAnea said: "There is a lot of enthusiasm among assistants to retrain, but not if they are only going to be paid a few hours a week to do it."
At the moment, each local authority sets wage levels for teaching assistants. On average, assistants earn around pound;13,500 a year, and HLTAs should be paid between pound;18,000 and pound;22,000.
Unison has drawn up proposed national pay scales, which would see teaching assistants paid up to pound;15,015, and HLTAs between pound;23,265 and Pounds 26,157 a year. Talks are about to begin with other support-staff unions -including the GMB and the Transport and General Workers' - to back the claim.
Ruth Kelly, the Education Secretary, said she would be willing to consider a new national pay deal.
But some Unison members say the union should pull out of the workforce deal. The call will be led by the Brighton branch, which has been at the centre of a bitter industrial dispute over pay.
Any move to withdraw would throw the deal into disarray after the National Association of Head Teachers voted to pull out earlier this year. The National Union of Teachers has always opposed the deal.
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