The threat comes as The TES has learned that ministers will pay off part of the redundancy bill at a school that will employ cheaper staff when it becomes an academy.
The NASUWT is contemplating industrial action at six of the 27 academies that they say are exploiting teachers by failing to adhere to national contracts.
It has written to Alan Johnson, the new education secretary, demanding academies - which can use their status as independent state schools to draw up individual contracts - adhere to national rules on hours, pay and union recognition.
The union is already threatening action at North Liverpool academy, when it opens in September. Some 26 staff at Anfield and Breckfield comprehensives, which closes this summer to make way for the new school, are being made redundant. The Department for Education and Skills is part-funding severance payments.
This week it emerged that some new staff with teaching responsibilities will be paid a fraction of an experienced teacher's wage. An advertisement on the academy's website for a "dance instructorteacher", who would "teach dance through the age range and organise exhibitions and shows", offers a salary of just pound;15,000.
Three pastoral "head of house", posts are advertised at pound;18,000. The academy says these "specialist support roles" will "not necessarily" be filled by teachers.
The Granada Learning Trust and the Liverpool university - joint sponsors of the academy - insisted negotiations over new pay scales and contracts were ongoing but said it was "not feasible" to merge two schools without job losses.
Julie Lyon-Taylor,Jan official at the Liverpool branch of the National Union of Teachers, said: "In the end, 26 teachers took so-called voluntary severance, but it was absolutely clear that there was no place for them at the academy. Many of them were in their 40s and 50s and may have spoken against the new regime."
A spokeswoman for Granada Learning said: "As with any school merger, it is not feasible to establish duplicative roles. However, we are working with both schools to retain as many staff as possible." She said that the severence payments will be met by the local authority and the DfES. The DfES insisted this week that all redundancies were voluntary.
Chris Keates, NASUWT general secretary, said: "The Government has spent three years developing a package of pay and conditions with unions that benefit teachers and help raise standards. Why are academies, which are supposed to be in areas of the highest need, allowed to deviate from them? In at least six academies, conditions are completely unacceptable.
"We hope we can receive a satisfactory outcome to this through negotiation, but if not we are prepared to ballot for industrial action."
Ms Keates said one academy had extended the working year by five days, others had imposed longer hours and required teachers to do lunchtime supervision and extra administration duties.
The Macmillan academy, Middlesbrough, and Haberdashers' Aske's Knights academy, south London, are believed to be among the six identified by the NASUWT.