The review, undertaken in the wake of the garda scandals, found the dysfunctional department has a "deferential relationship" with An Garda Siochana with a lack of proper accountability.
On foot of the report, the department's secretary general Brian Purcell, who played a pivotal role in the resignation of former Garda Commissioner Martin Callinan, was forced to stand aside from his position.
But Mr Purcell is not resigning and will take up a post elsewhere in the public service.
Ms Fitzgerald said there was "no secret deal" with Mr Purcell to prevent him from retiring.
The report doesn't specifically refer to the garda scandals, the management of the whistleblower affair or the taping fiasco, but it does cite "recent events" and says there were "serious leadership and management failures" in the Garda Division in the Department and senior management "regarding how briefings between the minister and senior management were handled".
The failings included no one person being in charge of the overall issues, no overall plan to deal with the issues as they unfolded, no recognition of the serious potential impact of the issues and an inability to see where things go wrong.
"There is a closed, secretive and silo culture which has inhibited the capacity of the organisation to questions and to challenge and therefore to learn and adapt," the report said.
Ms Fitzgerald said the report was "hard-hitting and critical".
"It's a very critical report but it's a constructive report and it maps a way forward for the department."
Fianna Fail said the damning report on the department highlights the dysfunction in administration of justice.
The party's justice spokesman Niall Collins said there needed to be significant personnel changes within the Department.
"Unfortunately this report cannot be looked at in isolation, we have already seen the Cooke Report and Guerin Report which led to the Fennelly Inquiry. All these were established as a result of mismanagement within the department."
A key recommendation of the report is the restructuring of the Department into "Justice and Home Affairs portfolios".
The Justice area will include civil and criminal law reform, crime and security, and international policy. Home Affairs will include policing, prisons, courts, equality and integration.
A new deputy secretary general would head up the Home Affairs side - but only one minister would be required.