A prominent Boeing whistle-blower, a former quality manager who raised concerns about manufacturing practices at the company’s 787 Dreamliner factory in South Carolina, was found dead on Saturday with what appeared to be a self-inflicted gunshot wound, according to local officials.

The whistle-blower, John Barnett, was in Charleston for a deposition for a lawsuit in which he accused Boeing of retaliating against him for making complaints about quality and safety.

Quality problems involving both design and manufacturing have plagued Boeing for years — most prominently after the crashes of two Boeing 737 Max jets in 2018 and 2019, and again since a fuselage panel blew out on a Max flight shortly after takeoff two months ago.

Mr. Barnett filed the complaint against Boeing with the U.S. Labor Department in 2017 under the AIR21 Whistleblower Protection Program, which protects employees of plane manufacturers who report information pertaining to air carrier safety violations. He left the company that year.

Boeing’s lawyer deposed Mr. Barnett on Thursday and he was questioned by his own lawyers for half the day Friday. They were scheduled to complete the deposition on Saturday morning, said Robert Turkewitz, Mr. Barnett’s lawyer in the case.

When Mr. Barnett, 62, did not show up on Saturday morning and did not answer phone calls, Mr. Turkewitz said he grew concerned and called Mr. Barnett’s hotel. Mr. Barnett was then found dead in his pickup truck in the hotel parking lot.