State Comptroller Micha Lindenstrauss submitted his annual report to Knesset Speaker Reuven Rivlin on Tuesday.
The report has been deemed "unprecedented in scope" and contains 64 chapters reviewing a broad array of state bodies.
The Defense Ministry and IDF under Ehud Barak, however, came under withering fire from Lindenstrauss who delivered blow after blow in his report.
The comptroller noted that assorted IDF organs failed to follow up on munitions acquisitions, causing a two-year delay for the army.
He also targeted the IDF failure to meet its enlistment quotas for the Hareidi sector while simultaneously turning away prospective volunteers due to relevant programs not being properly funded.
The report also detailed several failures in the decision-making process regarding the IDF's drone fleet, noting that the Defense Ministry and the Aerospace Industries "must review their protocols and collaboration and ensure that the existing controlling mechanisms are applied and reviewed.
"Both should also review the great investments needed to realize some of the projects and their impact on the defense budget."
He further faulted Israel Military Industries' protocols, saying that "Deciding on heavy munitions production sans budgetary backup from the government is a fundamental failure."
Lindenstrauss' also took aim at military export protocols saying, "Many operational failures have been found it at least five major deals."
Nor did Lindenstrauss stop there. He went on to charge that Defense Ministry officials, including its director general, had broken protocol.
"Given the innate sensitivity of military exports, a situation where laws and regulations are not followed, or when the Foreign Ministry is not consulted with, may seriously harm Israel's interest," he said.
He then went on to slam the government's failure to implement a plan to create a missile defense system for civilian planes.
The creation of such a system was ordered by former Prime Minister Ariel Sharon in 2003 following an incident late in 2002 in which missiles were fired at an Israeli plane over Kenya.
The Transpiration Ministry was tasked with heading the project, but failed to form a task force on the matter, or ever name specific individuals to oversee the various aspects of the project.
As a result, Prime Minister Benjamin Netanyahu decided to suspend the project in 2011, citing "implementation issues."
Lindenstrauss accused officials of "fumbling through it," writing, "despite this being a matter or national and security importance and that with each passing day the risk to civilian aviation grows, the Transportation Ministry still took five months to follow the PM's order."
"The fact that a great gap still remains between the intensity of the threat and that of its solution, is extremely grave," he wrote, noting the Transportation Ministry had failed to even decide on the basic concept for the system.
Lindestrauss also took aim at failings in Israel's Health Ministry, noting the ongoing wage conflicts with doctors and nurses, and ongoing staffing problems in Israel's hospitals.
"I have said on many occasions that the personal liability of those in the executive branch [of government] is the heart of good governance," Lindenstrauss said. Public servants "however senior, must take responsibility for their actions or failures."
Lindenstrauss added that his final report included a review of how to reduce the bureaucratic burden of public service.
"The role of government and the public sector is to serve the citizens of the state," Lindenstrauss said, noting that in many cases, his office had found that public bodies imposed a "heavy and unnecessary bureaucratic burden on business owners and residents," which he said "eroded public trust in public service."
The report will be Lindenstrauss' last, as he is set to retire. The Knesset will vote on his replacement on May 14.
Lindesntrauss denied previous reports he was interested in pursuing the Presidency.