The second biggest academy provider stands accused of mismanaging the budget of one of its schools, leading to class cancellations and staff redundancies.
Some 13 staff, or a third of the workforce, will lose their jobs at the MediaCity Oasis Academy in Salford.
The Nasuwt teaching union says the academy overspent by hiring expensive senior staff and consultants.
But the school, run by Oasis UK, blames government cuts and overstaffing.
Oasis UK, a Christian organisation, runs 11 secondary and two primary academies, apart from Oasis Academy MediaCity UK which opened three years ago.
Nasuwt members walked out of the school on Thursday for the fifth time in the latest strike over the redundancies.
Principal Patrick Ottley-O'Connor said in a letter to parents the school would be closed during the strike to all but Year 11 students who are preparing for exams next month.
A statement from the school confirmed that 13 members of staff are to lose their jobs, nine of whom are teachers.
In his letter to parents, Mr Ottley-O'Connor said the two sides had been unable to resolve issues around the staffing restructure and that a new lesson time-table will be issued next term.
But Nasuwt said the redundancies had come about because of "serious management failures"
Karen Hopwood, the union's representative for Greater Manchester, said the academy had hired two assistant heads on top salaries last summer, but announced the 13 redundancies in October.
And she claimed the school was spending too much money on supply teachers and expensive subject consultants.
Oasis UK said in a statement: "Due to a combination of inherent overstaffing and government cuts, it has been necessary to make redundancies ahead of our move to our MediaCity campus in September 2012."
The school is due to move into a brand new complex on the edge of Salford Quays next year with modern facilities.
A Department for Education spokesman said: "Academies are given complete freedom over their budgets and pay and conditions and we expect them to manage their own financial position.
"However, should an Academy get into financial difficulties then they should work with the Young People's Learning Agency to resolve the situation."
Last year the government's spending watchdog warned that the rapid expansion of England's academies risked being poor value for money.
In a report published in September 2010, the National Audit Office said much tighter monitoring of academy finances was needed.
It found that academies were spending significantly more per pupil than mainstream schools and that one in four were likely to require extra financial support from government.
The NAO also pointed out that in 2007-8 and 2008-9 there were 50% more senior staff on salaries of more than £80,000.
The government had already recovered £4.1m in overpayments from academies because of an overestimation of pupil numbers.
Nasuwt general secretary Chris Keates has written to the education secretary Michael Gove asking him to intervene in the Oasis dispute.
She said: "Had the school still been part of a local authority family of schools, I have no doubt the necessary short-term financial cushion could have been found."
"Questions need to be asked about how an academy was allowed to get into this situation."