All ballots held so far by the National Union of Teachers have backed action against the reform which could cut some teachers' pay by up to pound;10,500 per year.
It is the latest sign of growing union frustration with the way headteachers are implementing the switch from management allowances to teaching and learning responsibility payments.
The ballots by the NUT, the only union not to sign up to the workforce agreement, do not give it the right to call a strike because they were not conducted by the Electoral Reform Society.
John Dixon, assistant secretary, said the union has resolved problems in six schools so far through negotiation. The NUT hopes to avoid strikes but action could be taken before Christmas unless schools compromise. "The next three or four weeks will be interesting and very busy," he said.
The NASUWT, the largest teaching union to agree the changes with government, is also threatening action in four areas - Derbyshire, Southampton, Stoke-on-Trent and Worcestershire. It says these councils have advised school badly over TLRs.
Every school in England has to review its staffing by the end of December and decide who qualifies for TLRs which, unlike management allowances, cannot be given for administrative duties.
Management allowances worth between pound;1,163-pound;10,572 per year will be replaced by TLRs ranging from pound;2,250-pound;11,000. The changes were agreed as part of the workforce reform.
But the NASUWT believes some heads have not followed official guidance and instead used the staffing review to cut salary costs.
The result of the union's first formal ballot for action at Noel-Baker school in Derby is expected to be announced today.
Chris Keates, general secretary of the NASUWT, said the National Association of Head Teachers was causing a particular problem in primaries.
She said a number of heads were identifying responsibilities but refusing to pay for them. "That is unacceptable. The NAHT is supporting that."
Mick Brookes, NAHT general secretary, said: "We are giving technical advice to school leadership teams about how to implement the changes. Some people find TLRs a useful tool and for others it is a complete nightmare."
"The NASUWT is now reaping the rewards of what it and the other teacher unions signed up to. It comes as a bit of a surprise to us that they don't like it."