Nursery nurses, teaching assistants and other support staff in Sunderland have been told they must work more hours or face a pay cut.
Staff in Surrey, Reading and Lambeth, in south London, are thought to be facing similar problems.
Difficulties arise because a single status agreement which requires each local authority to place all council workers, including school support staff, on a single pay scale at a level appropriate to their job.
At present, teaching assistants and nursery nurses are paid a monthly salary for the hours worked during term time. They generally work 32.5 hours a week and say that this relatively low number means they should be classified as part-timers. They want to be paid more for hours over and above the norm.
But some local authorities believe teaching assistants and nursery nurses are full-time workers who are not working full-time hours and that it would be unfair on other council workers for them to get more money.
Sunderland council began implementing the agreement, which was supposed to create an equal and transparent pay scale for council workers last October.
Teaching assistants and nursery nurses in Sunderland say they feel undervalued and betrayed by the change, which could mean they lose pound;2,000 a year.
Earlier this month, members of the Professional Association of Teachers passed a motion at the union's annual conference calling for a national pay structure for nursery nurses and teaching assistants.
Gina Smith, 53, a nursery nurse working in Sunderland, who proposed the motion, said she considered her post and pay to be part-time.
She said: "They are trying to make out we are full-time employees but we are not. If they want us to work longer hours, our salary should be increased pro-rata, not decreased if we refuse."
A spokesman for the PAT said some local authorities, such as Gateshead, implemented the national agreement well and members would not have to take a pay cut. But support staff in other areas, including Surrey, Reading and Lambeth are experiencing problems.
Sue Stanhope, head of personnel at Sunderland council, said the Unison and GMB unions voted to accept proposals in February which included replacing previous agreements where nursery nurses worked part-time but were paid "as if they were full time".
She said: "This was discriminatory and had to be replaced. The council and unions agreed a number of measures to assist staff during this transitional period."
The unions said they had not let school support staff down by accepting Sunderland's proposals and that they would continue to fight to protect their members' pay.