The US aviation giant, which has struggled with manufacturing and quality control issues in recent years, reported a third-quarter loss of $1.6 billion, compared with a loss of $3.3 billion in the year-ago period.
The latest issue with the 737 is the result of misshapen holes drilled in a part of the fuselage that helps maintain plane pressure. Boeing said the problem is not "an immediate safety of flight issue."
However, the company is inspecting and reworking undelivered planes. As a result, Boeing now expects 737 deliveries of 375-400 this year, down from the earlier 400-450 projection.
Boeing's bottom line in the quarter was also affected by a $482 million loss in the Air Force One US presidential plane "related to engineering changes and labor instability, as well as resolution of supplier negotiations," Boeing said.
Another $315 million hit came from losses in a satellite contract, also in Boeing's defense, space and security business.
On the positive side, Boeing reaffirmed its outlook for free cash flow, a closely watched investor benchmark, and said it was on track with a plan to boost production on another jet, the 787 Dreamliner.
"We continue to progress in our recovery and despite near-term challenges, we remain on track," said Boeing Chief Executive Dave Calhoun.
"The important work we're doing to add rigor around our quality systems and build a culture of transparently bringing forward any issue, no matter the size, can bring short-term challenges -– but it is how we set ourselves on the right course for our long-term future."
Shares of Boeing rose 3.3 percent in pre-market trading.
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