(CNN) The Defense Department's first ever agency-wide financial audit discovered problems that cost approximately $559 million to fix, the Pentagon said Thursday.

"We spent approximately $406 million on audit remediation and $153 million on financial system fixes," the Department of Defense's statement on the audit read.

Several organizations -- including the Amy, Navy, Air Force, Marine Corps, the Defense Logistics Agency, US Special Operations Command and US Transportation Command -- received "disclaimers," which "means they have multiple issues that need to be fixed," the statement said.

The problems centered on inventory accuracy, property and compliance pertaining to cybersecurity.

"We failed the audit but we never expected to pass it," Deputy Secretary of Defense Patrick Shanahan told reporters at the Pentagon on Thursday.

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