The Education Department says reviews done last year and in 2010 have raised questions over use of funding and governance practices by the Council of African Canadian Education.
The province says a review completed this summer found the Halifax-based council was operating outside its legislative mandate.
The review also found reporting structures are applied inconsistently and without proper documentation.
It says there are inconsistencies in financial reporting.
The council could not be reached for comment on the province's review and the plans for the audit next year.