Ministers announced last week that about one million temporary workers, including supply teachers, would be entitled to equal treatment after 12 weeks in a job.
For most commercial temps, this means their pay will be increased to bring it into line with their full-time, permanent colleagues.
But Select Education, the biggest education recruitment agency, said some less experienced or overseas-trained teachers could expect their pay to drop after 12 weeks because they had been receiving more than equivalent full-time staff.
Most large supply agencies hire out teachers according to supply and demand, so a physics teacher in London can earn more than an English teacher in Yorkshire. They are not generally paid according to their grade on the national scale.
In London, a head will pay an agency pound;150-pound;175 a day for cover; the teacher will receive pound;110-pound;130.
John Dunn, a director of Select Education, said: "You might have the perverse situation of someone asked to take less pay after 12 weeks."
Barry Fawcett, head of pay for the National Union of Teachers, warned that if staying to the end of term meant a pay cut, supply teachers would take a new job instead.
The deal for temporary staff was negotiated by the Government, the Confederation of British Industry, and unions. Some employer groups fear businesses will no longer be able to afford to hire temps. But Mr Dunn said Select did not expect reduced demand for supply teachers.
Czeslaw Krupski, an experienced secondary English and history teacher who has been doing supply work for the past four years, welcomed the plan. As a senior teacher, he expects to be paid on the upper pay scale after 12 weeks, which means his pay would go up to about pound;150 a day.
"A number of supply teachers do the job for many years without any improvement in their pay and conditions," he said. "This will cast light on a dark area - the role of the supply teacher in education."