The latest problem with the F-35 Joint Strike Fighter? There might be something seriously wrong with the gold-plated aircraft’s brain.

A Government Accountability Office report released Thursday raises concerns about the jet's $16.7 billion Autonomic Logistics Information System (ALIS). The software is essentially the brain that enables the fifth-generation warplane to operate, tracking everything from the amount of time the aircraft spends in the air to when the engine needs a tune-up.

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The roughly $400 billion F-35 effort has had more than its share of software hiccups already, highlighted by recent findings that the aircraft’s billions of lines of computer code might be vulnerable to hacking.

If the bugs persist, it could have a cascading effect on the rest of the Defense Department’s timeline for the warplane, which is already years behind schedule. Serious problems with the logistics system could delay important program milestones, including the U.S. Air Force declaring its version of the jet ready for deployment later this year.

In its report, GAO identified two major problems with Lockheed Martin’s ALIS, the first being that the system itself may not be deployable.

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The ALIS tool gets plugged into a jet, sending data to two 1,600-pound sever racks. Each F-35 squadron requires its own set of ALIS computers, making it difficult to operate since it “requires server connectivity and the necessary infrastructure to provide power to the system,” according to the new report.

Last year the Marine Corps, which often deploys to remote locations, declared its version of the F-35 ready for deployment “without conducting deployability tests of ALIS.”

A slimmer version of ALIS that can fit into moveable cases -- capable of being carried by two men and weigh approximately 200 pounds each -- was put into operation last summer. However the Pentagon “has not yet completed comprehensive deployability tests,” the GAO report states.

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The second key issue is that there’s no alternative to ALIS if there’s a problem. That lack of redundancy is compounded by the fact that all ALIS data is fed into a “central point of entry” and then to an operating unit in Fort Worth, Texas.

“If either of these fail, it could take the entire F-35 fleet offline,” GAO warns.

The report also raised concerns about the system’s inability to communicate with the systems aboard older aircraft, and noted that ALIS users are worried about transferring data between classified and unclassified computer servers.

The watchdog office suggested the Pentagon develop a “holistic” plan to address myriad issues with ALIS to make sure biggest problems with it are taken care of before the F-35 enters full production in the early 2020s.