A Muslim school turned away new governors after the council launched a take-over following persistently poor teaching and management.
Staff at Al-Hijrah School in Birmingham refused to co-operate when members of an interim governing board arrived on Thursday, according to council education bosses.
Birmingham City Council decided to remove the existing governors at the city's only Muslim school, replacing them with its own team, after Ofsted snap inspections revealed a "serious decline" in classroom standards.
The school, in Bordesley Green, is not one of the 25 which have been inspected as part of the city-wide Operation Trojan Horse investigation over allegations of a hardline Muslim plot to seize Birmingham schools.
In a letter to current governor Waseem Yaqub, Peter Hay, the council's strategic director for people, said: "The time for debate is over, the children in Al-Hijrah need governors that govern the school properly."
Referring to the blocking of the new governors on site last week, Mr Hay wrote: "Yesterday, the school and governors did not co-operate with the implementation of the new governing body."
He said the council would try again to install the new leadership on the first day of the new term, urging co-operation from Mr Yaqub and his fellow governors - and making it clear they no longer have any authority to run the school.
Al-Hijrah was placed in special measures after an inspection in December 2013, but after a follow-up visit in April this year Ofsted found "governance remains inadequate".
Among the criticisms, inspectors said the the governing board were "not addressing the key weaknesses across the school".
It said chairman of the board Mr Yaqub had told inspectors he thought the school was being targeted "by a witch hunt".
Pointing to a breakdown in the school's relationship with the council, Ofsted said: "Recent attempts by a local authority officer to visit the school have been thwarted by senior leaders."
The report also revealed the governors had commissioned architects to design a new school building, despite a current budget deficit running at £400,000.
It emerged when the governors were unhappy with those figures, they spent £6,000 on a new audit to double-check the financial position.
Ofsted said the school's improvement plan to dig itself out of financial trouble was "not fit for purpose", but also criticised the council for having "not been able to support or challenge the school".
The school, which caters for four to 16-year-olds, receives taxpayer money as a voluntary aided school.
A Birmingham City Council spokesman said: "Following a series of inspections by Ofsted, which showed a serious decline at Al-Hijrah school that requires urgent improvement, a recent monitoring visit found that there were still continued failings relating to the school's governance, financial stability and its improvement plan.
"The Department for Education (DfE) approved the city council's application to appoint an interim executive board (IEB) and disband the previous governing body, which no longer has any powers or responsibilities in relation to matters relating to Al-Hijrah school.
"On May 22 members of the IEB visited the school, but withdrew when it became clear that staff there were not going to co-operate.
"The IEB will return to the school on Monday, June 2 to meet with staff and parents to inform them of the current situation."