The Defense Department’s F-35 fighter jet program has recently made progress on several fronts, but still faces “considerable” challenges and risks, according to a new analysis from government auditors.

The Joint Strike Fighter program in 2012 met most of its management objectives, according to recent testimony from Michael Sullivan, director of acquisition and sourcing management at the Government Accountability Office, the investigative arm of Congress.

The development effort last year completed initial software testing, started pilot training and renegotiated the contract with Lockheed Martin Corp., the plane’s manufacturer, yet failed to deliver the planned 40 production aircraft and correct deficiencies in the system for tracking cost and schedule progress, according to the remarks.

With about two-thirds of development testing remaining, “the program continues to incur financial risk,” Sullivan said in testimony prepared for a June 19 hearing of the Senate Appropriations Defense Subcommittee.

The Joint Strike Fighter is the Pentagon’s most expensive weapons acquisition program, with an estimated cost of $391 billion to develop and build 2,457 Lightning II aircraft. That’s $4.5 billion, or 1.1 percent, less than a projection from last year due in part to revised labor rates.

Fifty-two aircraft have been delivered through 2012. The single-engine jet designed to replace such aircraft as the F-16, A-10, F/A-18, and AV-8B.

The Defense Department next year plans to spend $8.4 billion to buy 29 F-35s, including 19 for the Air Force, six for the Marine Corps, and four for the Navy. The funding includes $6.4 billion in procurement, $1.9 billion in research and development, and $187 million in spare parts.

Ensuring that the F-35 is affordable continues to be “of paramount concern,” Sullivan said. The program is estimated to cost, on average, $12.6 billion a year through 2037, he said.

“Maintaining this level of sustained funding will be difficult in a period of declining or flat defense budgets and competition with other ‘big ticket items’ such as the KC-46 tanker and a new bomber program,” Sullivan said.

If international customers don’t buy the planned minimum of 697 aircraft, unit costs will increase. In addition, the Pentagon has said the cost to operate and sustain the jet — estimated at more than $1 trillion over its 30-year service life — isn’t affordable.

According to the GAO’s Sullivan, the program has made “considerable progress” in limiting the aircraft’s four areas of technical risk, including the helmet-mounted display, autonomic logistics information system, arresting hook system and structural durability. “However, additional work remains to fully address those risks,” he said.

Rep. Tammy Duckworth, D-Ill., earlier this month unsuccessfully sought to freeze procurement funding for the program until Defense Secretary Chuck Hagel certified that Lockheed fixed these problems.

“I want contractors to be held accountable and I want to fix the technical problems before we give them another $6 billion of taxpayer money,” she said during a hearing to amend the House’s version of the 2014 defense authorization bill. “There’s nothing wrong with flying before we buy. In fact, most of us test drive cars before we [buy].”

The panel voted against her amendment to the legislation, which sets policy goals and spending targets for fiscal 2014, which begins Oct. 1.

The program has also taken steps to improve the plane’s software, an area of concern that Pentagon officials and lawmakers have said may cause more delays, according to Sullivan.

Lockheed has reassigned 200 engineers to work on the software, including many from outside the aeronautics division, with specialties in space, ship-board, and sensor technology, according to Steve O’Bryan, vice president of F-35 program integration and business development.

“We pulled the best and brightest from throughout our organization,” he said June 19 during a press conference at the Paris Air Show.

The company has also invested $100 million to build a second laboratory where employees work in shifts around the clock to write, test, and verify the code, O’Bryan said.

The GAO found that the time it took to fix software defects last year fell from 180 days to 55 days and the time needed to build and release software for testing dropped from 187 hours to 30 hours, according to Sullivan.

Still, the version of software needed by the Air Force and the Navy to begin combat operations in 2016 and 2019, respectively, remains one of the program’s “highest risks,” he said. (The Navy on Saturday received its first F-35C, the version of the aircraft designed for carrier take-offs and landings.)

The final software package, known as 3F, is designed to support a suite of internal and external weapons, including the GPS-guided Joint Direct Attack Munition, laser-guided Paveway II bomb, Advanced Medium-Range Air-to-Air Missile, and infrared Sidewinder missile.