Advanced skills teachers in primary schools are paid 14 per cent less than their secondary counterparts, official figures show.
A Department for Education and Skills survey highlights a noticeable difference in the salaries of the so-called "superteachers", who earn between pound;29,757 and pound;47,469.
The disparity can be partly explained by differences in school size and pay differentials between the two sectors. But in a report to the independent pay review body, the DfES says: "Even within the limited range of salary points used for primary ASTs, the majority of posts attract pay in the lower half of that range."
It suggests that pay could be being artificially held down, particularly in primary schools, by an attempt to preserve differentials with leadership grades. There could also be a reluctance to offer what could be perceived as unsustainably high salaries when overall school funding was under pressure.
The Government introduced ASTs in 1999 as an alternative career path for excellent teachers.
The scheme was designed to encourage them to remain in the classroom rather than taking up management positions. There are now around 3,500 ASTs in England.
But the DfES survey showed that many teachers viewed the AST scheme as a stepping stone to management, with a third of those leaving it ending up in leadership positions.
Its findings are included in evidence submitted to the School Teachers' Review Body this month and are based on a survey of 1,070 ASTs, conducted between May and July 2003.
The findings will be used by the review body to help decide whether to recommend any changes to the pay structure in its forthcoming report, due to be published next month.
The survey found that 28 per cent of ASTs eligible for a performance pay rise had not received one.
A third of those leaving the scheme had been promoted with roughly the same number now in management positions.
And a further third who made additional comments on the survey said that their salaries did not reflect their responsibilities.
John Bangs, head of education at the National Union of Teachers, said: "It is surely impossible for Government to continue a two-tier AST pay system where primary teachers come off worst."
In its evidence to the review body, the DfES also argues for an end to the external assessment of decisions about which experienced teachers should cross the threshold on to the upper pay scale.
It said it could not justify spending pound;10 million a year verifying threshold decisions and that the process should be "embedded" in school performance management systems.
The DfES argues that with only 17 per cent of teachers now demanding a review of decisions, and only 23 per cent of those having them overturned, internal grievance procedures should be sufficient.
The main classroom teacher unions claim that it is the threat of an external review which discourages schools from making arbitrary threshold decisions and that it should remain in place.