Lockheed Martin via Reuters The Marine Corps' version of the Joint Strike Fighter, the F-35B, in a test run over Maryland in February 2012.

Hundreds of problems continue to plague the troubled Joint Strike Fighter, potentially calling into question the basic performance and reliability of the costliest weapons program in U.S. history, the Defense Department's inspector general charges in a new report.

In a 16-month investigation that began in February 2012, the inspector general's office — an agency within the Pentagon responsible for investigating allegations of waste, fraud, security lapses and other misconduct — identified more than 360 quality "issues" with the F-35 Lightning II — with 147 of them classified as "major."

The report, which was published Monday — hours before the U.S. government shut down because of congressional infighting — blames "ineffective" oversight by the Pentagon's F-35 Joint Program Office and the Defense Contracts Management Agency that failed to catch lapses by chief contractor Lockheed Martin Aeronautics Co. and numerous subcontractors — issues it said "could adversely affect aircraft performance, reliability, maintainability and ultimately program cost."

"The government incurred and will continue to incur a significant cost for these issues," the IG concluded.

The Joint Strike Fighter — a stealth multi-role fighter that's intended to be the main tactical jet for the Air Force, the Navy, the Marines and many of the U.S.'s allies — has had a troubled history.

It has been grounded at least four times for manufacturing problems, most recently in February, and it now isn't projected to start flying missions until 2018 — seven years behind schedule.

Meanwhile, its manufacturing cost has ballooned to about $392 billion, almost 70 percent above the original estimate projected 12 years ago, and the Pentagon estimates total long-term operating costs at more than $850 billion.

July 14, 2013 — Critics say the F-35 Joint Strike Fighter program is an over-budget, behind-schedule boondoggle; supporters say it's on-track and necessary to ensure continued U.S. air superiority.

A draft of the report has been pinging back and forth for months between the inspector general and the Joint Program Office. In the version published Monday, the IG's office said it was asking the F-35's overseers to try yet again after it disagreed with seven of the 13 responses they sent back to the most recent draft.

Among many other oversight and cost-control problems, the published report accuses the Joint Program Office, Lockheed and its subcontractors of:

Insufficient rigor in design, manufacturing and quality assurance, creating "an elevated risk of delivering nonconforming aircraft to the warfighter."

Failing to implement critical safety programs, posing "an increased safety-of-flight risk."

Employing dozens of project employees whose training certifications had expired.

Failing to "flow down" quality and technical requirements to subcontractors, leading to construction of "F-35 products that may not meet intended performance and reliability requirements."

The program's planning and processes "remain immature," the report charges, and "assembly instructions require immediate updating."

Lockheed and the F-35 oversight office responded that they had satisfied most of the complaints in the past year. But the IG found seven of their 13 responses inadequate and set an Oct. 28 deadline to fix them.

Related: Read the entire inspector general's report (.pdf)

In one of the "insufficient" responses, the Joint Program Office punted responsibility for pre-production testing of vendor components to Lockheed, saying such testing wasn't its responsibility and that it would cost taxpayers too much, anyway.

It also opposed the report's call to set up an independent quality control office for the F-35, saying it would be redundant — an assessment the IG disagreed with.

And to the IG's complaint that there was no evidence of any risk-based assessments of "high-risk" components, the report rejected the Defense Contracts Management Agency's offer to update its documentation. Instead, it demanded specifics on oversight at every contractor facility involved in the Joint Strike Fighter program.

The Defense Department was unavailable to comment on the report because of the federal government shutdown.

But in a statement released before the shutdown, the Joint Program Office argued that it had resolved 78 percent of the issues raised in earlier drafts of the report.

"A majority of the findings are consistent with weaknesses previously identified by the Defense Contract Management Agency (DCMA) and the F-35 Joint Program Office (JPO), and do not present new or critical issues that affect the health of the program," it said.

Lockheed claimed that the report was "based on data that's more than 16 months old," saying in a separate statement that "a majority of the Corrective Action Requests identified have been closed."

"When discoveries occur, we take decisive and thorough action to correct the situation," it said. "Our commitment is to deliver the F-35's world-class Fifth Generation fighter capabilities to the warfighter on time and within budget."

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