The plane maker on Tuesday said it would temporarily slow Dreamliner production to address the new issue and gradually increase monthly output to its target of five a month.

“We will continue to take the necessary time to ensure Boeing airplanes meet the highest quality prior to delivery,” the company said.

Boeing shares fell 3% Tuesday to $231.10 and were the worst performer on the Dow Jones Industrial Average.

Boeing halted handing over Dreamliners to airlines in late May, after federal air-safety regulators declined to approve the plane maker’s proposed method of inspecting the jets for previously disclosed production defects. It was the second such pause in the past year.

The Federal Aviation Administration said the newly discovered quality issue on certain 787s posed no immediate safety threat. While the agency will determine whether to require modifications to 787s already in service, the FAA said: “Boeing has committed to fix these airplanes before resuming deliveries.”

The current Dreamliner delivery halt follows a five-month delivery pause from last fall through this spring. That led to a pileup of around 100 planes by the end of April, many of which Boeing had hoped to deliver by year-end. Boeing said Tuesday it expected to deliver less than half its 787 inventory this year. It delivered 14 Dreamliners as of the end of June.

The delivery pause is another setback for the aerospace company, which has been grappling with various problems in its commercial, defense and space programs in recent years. It is also choking off an important source of cash as Boeing tries to overcome twin crises that resulted from two fatal crashes of its 737 MAX aircraft in late 2018 and early 2019 and the Covid-19 pandemic’s hit to aircraft demand.

The new problem surfaced on part of the aircraft known as the forward pressure bulkhead at the front of the plane, people familiar with the matter said. It involves the skin of the aircraft and is similar to a previously disclosed Dreamliner issue found elsewhere on the planes, one of these people said. It surfaced as part of the FAA’s review of Boeing’s quality checks on newly produced, undelivered planes, this person said.

Engineers at Boeing and the FAA are trying to understand the defect’s potential to cause premature fatigue on a key part of the aircraft’s structure, people familiar with the matter said.

In late May, Boeing again halted Dreamliner deliveries after the FAA declined to approve the plane maker’s proposed method using a mix of analysis and physical inspections to check newly produced Dreamliners for quality problems. The agency requested more data to back up Boeing’s proposal.

Boeing’s recent 787 production problems arose last year. A combination of defects prompted Boeing to voluntarily ground eight of the planes in service. The FAA launched a broad review of the manufacturer’s factory processes. Boeing widened its inspections and eventually resumed deliveries in late March before halting them again two months later.

Write to Andrew Tangel at Andrew.Tangel@wsj.com