Heads and deputies want the gap between their pay and salaries of classroom teachers to be widened to reflect their greater burden of responsibilities.
The National Association of Head Teachers has told the School Teachers' Review Body that wage increases for classroom teachers mean there is too little incentive for them to seek promotion.
It says many primary teachers at the top of the pay scale will get annual salaries of around pound;34,900 from September because of increases and management allowances.
Typical primary schools offer salaries of around pound;33,000 to pound;36,000 for assistant heads and pound;34,000 to pound;37,000 for deputies.
The union argues that the narrow gap, created by faster improvements in pay for classroom teachers, has exacerbated shortages of senior staff.
David Hart, NAHT general secretary, said: "Pay differentials between school leaders and the rest of the teaching profession have been shot to pieces.
"Their salaries no longer reflect the very significant responsibilities they carry.
"The vast majority of classroom teachers have benefited from performance-related salary movements. Our members are in grave danger of falling behind."
The pay review body is due to make recommendations this autumn on the pay teachers should receive from September 2006 to August 2008 and is now taking evidence.
Unions which have signed the workforce agreement are still preparing their joint submission to the Government.
The NAHT and the National Union of Teachers, which have pulled out of the deal, have put in separate submissions.
The NUT, the largest teachers' union, is pushing for a pay increase for all teachers of 10 per cent or pound;2,500, whichever is the greater.
It is also calling for extra allowances for teachers in inner London, outer London and fringe areas near the capital of pound;6,800, pound;4,500 and pound;3,400 respectively.
The union said many teachers have had a pay cut in real terms since April last year because of inflation and the decision to freeze increases in management allowances. It argues against linking pay to the amount of time teachers spend training and collaborating with others, an idea suggested by Ruth Kelly, the Education Secretary.
Andy Inett, assistant director of the National Employers' Organisation for School Teachers, said schools had flexibility to move deputy heads up the pay spine if they wanted to, so there was no need for an across-the-board rise.
He said there may also be cases where an overlap of pay between senior classroom teachers and deputies is justified, and he would not want to deny schools this option.