The culture in primaries means that many are missing out in the new pay arrangements, the union's annual conference in Belfast next week will hear.
Some primary staff are also failing to benefit from moves to reduce teachers' workload, which have relieved the pressures on many.
Chris Keates, the NASUWT's general secretary, said: "People feel that because they are in a small school, they shouldn't get an additional payment. But when the pay arrangements were devised, the size of the school wasn't a factor."
The NASUWT, with other unions, the Government and employers, was involved in working out the system of teaching and learning responsibility payments, which came into force in 2005.
Mrs Keates said the problem had become "a lingering issue" of the review of staffing structure.
She said that too many primary teachers were not feeling the effects of workforce remodelling because some governors and heads were treating it merely as a "paper exercise". The majority of schools had complied contractually with the agreement, she added, but this did not always translate to the experience on the ground.
Some schools had succeeded in reducing workload by reducing duties such as cover, only for the void to be filled with excessive planning and assessment regimes related to Ofsted, said Mrs Keates.
Last year, 132 schools voted for industrial action over responsibility payments. The NUT said all its primary school disputes have since been resolved. The NASUWT has four outstanding, none which have led to strike action.
At the tiny St Wenn school in Cornwall, Andrew Brook refused to continue his work as head of three subject areas after he was denied an extra responsibility payment. He has since struck a deal with the school.
Staff at Holy Spirit primary in St Helens, Merseyside, went on strike last year after finding out their five management allowances would be replaced with two responsibility payments. The NASUWT said the situation now required constant monitoring.
John Rimmer, the NASUWT member for the North West, said many teachers were afraid to "put their heads above the parapet" to fight for responsibility payments. "They are afraid of victimisation or not getting a good reference. It can be very, very stressful," he said.