Academies are paying school heads more than in maintained schools, but classroom teachers less.
That finding comes from Department for Education workforce data, based on average figures.
The average salary for a classroom teacher in a local authority maintained secondary school was some £1,400 a year higher than in secondary academies.
But an academy headteacher received £92,589, compared with £90,759 for their maintained school counterparts.
Maintained secondary schools paid leadership teachers on average £64,415, slightly more than the £64,106 paid by academies.
For classroom teachers, academies paid £37,356 and maintained schools £38,829.
NEU general secretary Mary Bousted said: “To have two school systems with such a differential in what teachers are paid is unacceptable.
“Being a school leader is a difficult job, but so is being a teacher.”
Chris Keates, NASUWT general secretary, said the pay differential between academies and maintained schools was “something we have consistently highlighted.
"It is a consequence of the excessive freedoms and flexibilities given to schools which are then used to fuel a race to the bottom in teachers’ pay."
Ms Keates added: "It is hardwired into the system thanks to this government’s policies that you pay teachers what you can get away with rather than recognising that teachers' pay and conditions of service are inextricably linked to high-quality education."
There was a similar pattern in the primary sector, where academy heads were paid an average of £65,963 and maintained school heads £64,280.
Leadership teachers did better in maintained schools, being paid £56,018 and those in academies £55,218.
Primary classroom teachers were again better off in the maintained sector, receiving £35,249, against £33,442 for academies.
Data from the same set of statistics has also shown that female headteachers get paid less on average than male headteachers at every type of school.
Male teachers earn £36,900 on average, compared with £36,000 for female teachers – 2.5 per cent more. But for headteachers the gap widens, with men earning £75,500 on average, while women get £67,400 – a 12 per cent gap.