Teachers fear they may be paid less and have their rights undermined as more English secondary schools become city academies, unions say.
The independent academies can opt out of national pay negotiations and set their own curriculum, despite being largely state-funded.
Unions claim some teachers have had to sign "gagging clauses" with many afraid to question conditions.
The Department for Education and Skills said academies were working well.
Schools in deprived urban areas can apply to become academies if they raise £2m from private sponsors.
The government then tops this up, typically by about £25m.
The NASUWT union will present reports from its representatives at seven of the existing 17 academies to ministers this week.
They say some are trying to bypass unions in negotiations.
Some are causing staff to work longer hours and supervise lunch hours, according to documents seen by the Guardian newspaper.
The union confirmed the content of the documents but declined to discuss it.
Two academies had asked staff to sign clauses to stop them "disclosing academy business".
Meanwhile, John Bangs, head of education at the National Union of Teachers, told BBC News: "There is a high level of anxiety about stepping outside the academies' boundaries.
"It's an undermining of teachers' union rights."
Some academies were doing deals with unions, while others were being less co-operative, he added.
Mr Bangs said: "It has not happened yet, but there is the potential for the academies to reduce their pay and conditions requirements."
With the increasing cost of setting up new academies, he also questioned whether the £2m raised by sponsors should entitle them to the level of autonomy they have been granted.
The government wants 200 of the flagship schools to be built or under way by 2010.
This summer the proportion of pupils at city academies gaining the equivalent of five or more GCSE grades A* to C was 27.4%.
A Department for Education and Skills spokeswoman said: "Academies have this freedom of flexibility to help them improve standards in areas of considerable social and economic deprivation, and they are working."