The Belfast board has overspent by more than £5m
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The chief executives of two education boards were in "very serious breach" of their responsibilities as accounting officers, an investigation has found.
The South Eastern and Belfast boards ran up large deficits prompting the government to announce an inquiry.
That has found weaknesses and failings in dealing with financial issues.
The report said the chief executives should not lose their jobs, but they have been put on probation as accounting officers until next June.
The statutory inquiry was led by Dr Bill Jack, the former comptroller and auditor general at the Northern Ireland Audit Office.
It looked at how the deficits came about without any apparent forewarning to the members of each board.
In its report, the inquiry team pointed out that board members should challenge staff more on finance.
The Department of Education also said there was no need to take action against board members or chairmen.
The report was laid before parliament on Monday by the Northern Ireland Education Minister Barry Gardiner, who said he had accepted its findings in full.
He said: "The report highlights serious failings in the execution of responsibilities within both boards and makes 49 specific recommendations for improvement relating to each board, its chief executive and chief finance officer.
Action plan
"The report gives a very powerful assessment of the failures in financial management in these two boards. The lessons it highlights are relevant across all of the five boards."
Mr Gardiner said it was estimated that the South Eastern board had now overspent by £21.4m and the Belfast board by £11.4m.
The minister is to discuss the report with the heads of the two boards later on Monday, and will urge them to produce an action plan to implement its recommendations.
Mr Gardiner announced the inquiry last November when he vowed to "get to the bottom" of how both boards ran up the huge deficits.
He said the inquiry would focus on the effectiveness of the financial control systems in place in each board.