Joanne Bernard said she has had trouble finding out from groups that receive the money who they serve and what difference their services make in the community.
"This isn't pinpointing anybody," Bernard said. "This merely is a review that is long overdue and really hasn't been done in this department."
Bernard said there is about $10 million to $12 million in discretionary funding that is given annually to hundreds of organizations across the province and she wants to ensure that Nova Scotians get the best use of those funds.
She said the review won't mean organizations will be cut "off at the knees," but it will see her department work with groups in order to establish measurements to evaluate their services.
Acting NDP Leader Maureen MacDonald said while accountability is important, Bernard is creating uncertainty by suggesting there are potential problems.
"What I'm concerned about is that legitimate groups are going to have to participate in a process to justify what they legitimately do," said MacDonald.
Bernard, who worked as the executive director of Alice Housing and held positions on a number of non-profit boards prior to her election last fall, said the review should take about six months to complete.