Financial systems were "weak" and information given to the South Eastern Education Board "inaccurate", a report on its finances has said.
The education board members refused to pass cuts
However, the commissioners running the board said its new chief finance officer and her team were making "significant improvements".
Consultants were appointed by former SEELB board members concerned about how the finances were being run.
They were stood down by the Department of Education for not cutting costs.
However, the financial probe continued under commissioners sent in to run the board by the department.
BBC Northern Ireland education correspondent Maggie Taggart said the report was the latest in a series looking into finances at the board and it "spells out the faults".
"They include poor financial systems and insufficient staff in the finance department," she said.
"However the report complimented the work of the new chief executive, Irene Knox, and the board members, those same people who have now effectively been sacked.
"The commissioners say the work is ongoing and they will be vigilant in monitoring improvements.
"They say they still need to look at some issues, such as the deficits in some schools' budgets."
The government put four commissioners in charge of the South Eastern Education and Library Board when its members refused to implement extreme budget cuts.