By Doug Cameron 

Boeing Co. said it uncovered more issues with its new military tanker aircraft, tripling the total pretax charges from the troubled program to more than $1.2 billion so far as it works to meet its delivery target for the U.S. Air Force.

The company on Friday said ground tests of the KC-46A Pegasus tanker's fuel systems during the second quarter revealed parts that didn't meet Air Force specifications, forcing new design and manufacturing work and triggering an $835 million pretax charge.

The Pegasus--a heavily modified version of Boeing's 767 commercial jetliner--is designed to be the U.S. Air Force's main aircraft for refueling other planes in midflight, replacing planes with an average age of 50 years. Boeing in 2011 won a contract to produce 179 Pegasus jets, following a decadelong contest with Airbus Group SE.

The $41 billion tanker program is one of Boeing's largest defense contracts, and a driver of sales as it pursues a deal to build a new long-range bomber for the Air Force--a program expected to cost at least $80 billion--ends production of older transport planes and faces an uncertain future for combat jets. However, Boeing's aggressive bid for the Pegasus deal left it on the hook for any cost overruns, and nursing a loss on the first batch of 18 aircraft.

Boeing executives had recently indicated the Pegasus was back on track after wiring and software problems last year delayed test flights and forced it to take a $425 million pretax charge on the program.

The latest charge equates to $536 million after taxes, which Boeing said will wipe 77 cents from per-share earnings when it reports on July 22. The company said its 2015 revenue and cash flow guidance remained unchanged.

The coming quarterly earnings report also will be the first for Dennis Muilenburg since he took over as Boeing's chief executive on July 1 after serving as president and chief operating officer, as well as head of its defense business when it was awarded the Pegasus contract.

Boeing shares were down about 1% in midafternoon trading Friday.

Boeing said it remained confident of meeting its commitment to deliver 18 planes to the Air Force by its contracted August 2017 target.

The Air Force said it also was optimistic Boeing would meet that deadline. "While we have more heavy lifting coming up, we believe it is achievable and do not see any technical showstoppers," Gen. Duke Richardson, the military head of the tanker program, said.

Boeing Defense and Space President Chris Chadwick in February centralized oversight of its large programs, including the Pegasus and the replacement for Air Force One. The move was designed to cut costs, keep projects on schedule and avoid a repeat of the tanker problems, though executives said it was also meant to help its pitch for the bomber.

Boeing is teamed with Lockheed Martin Corp. and faces competition from Northrop Grumman Corp. for the bomber, with an award expected in September.

The initial bomber deal will be a cost-plus contract that sets a cap on contractor's expenses and keeps most of the risk with the Pentagon, but the Defense Department is increasingly pushing for more fixed-price deals such as the tanker to motivate defense contractors. Such arrangements are similar to contracts in the commercial jet business, where airlines often order aircraft not yet designed but aren't required to cover any additional development costs.

The latest Boeing charge "is another reminder of how financially perilous it is for defense [companies] to take on fixed-price development contracts," said RBC Capital analyst Robert Stallard of the latest Boeing charge.

A Pegasus test aircraft made its first flight last December, some five months behind schedule. The full version, complete with fueling boom and military systems, is expected to fly for the first time in September.

Boeing also is pushing the Pegasus with international customers, though Airbus has enjoyed more success securing deals with a tanker version of its A330 jet.

Write to Doug Cameron at doug.cameron@wsj.com

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