In an extraordinary on-air rebuke, one of the top journalists at “60 Minutes” directly criticized the program’s parent company in the final moments of its Sunday night CBS telecast, its first episode since the program’s executive producer, Bill Owens, announced his intention to resign.

“Paramount began to supervise our content in new ways,” the correspondent, Scott Pelley, told viewers. “None of our stories has been blocked, but Bill felt he lost the independence that honest journalism requires.”

A spokesman for Paramount had no immediate comment, and has previously declined to comment on Mr. Owens’s departure.

Mr. Owens stunned the show’s staff on Tuesday when he said he would leave the highest-rated program in television news over disagreements with Paramount, CBS’s corporate parent, saying, “It’s clear the company is done with me.”

Mr. Owens’s comments were widely reported in the press last week. The show’s decision to repeat those grievances on-air may have exposed viewers to the serious tensions between “60 Minutes” and its corporate overseers for the first time.

Shari Redstone, the controlling shareholder of Paramount, has been intent on securing approval from the Trump administration for a multibillion-dollar sale of her media company to a studio run by the son of Larry Ellison, the tech billionaire.

President Trump sued CBS last year, claiming $10 billion in damages, in a case stemming from a “60 Minutes” interview with the 2024 Democratic presidential nominee, Kamala Harris, that Mr. Trump said was deceptively edited. Ms. Redstone has expressed her desire to settle Mr. Trump’s lawsuit, although legal experts have called the case far-fetched.

In his remarks on Sunday night’s telecast, Mr. Pelley presented Mr. Owens’s decision to resign as an effort to protect “60 Minutes” from further interference.

“He did it for us and you,” Mr. Pelley told viewers of the show, which began airing in 1968. “Stories we pursued for 57 years are often controversial — lately, the Israel-Gaza War and the Trump administration. Bill made sure they were accurate and fair. He was tough that way. But our parent company, Paramount, is trying to complete a merger. The Trump administration must approve it.”

After “60 Minutes” ran a segment in January about the war between Israel and Hamas, Ms. Redstone complained to CBS executives about what she considered the segment’s unfair slant. A day later, CBS appointed a veteran producer to a new role involving journalistic standards. She reviewed certain “60 Minutes” segments that were deemed sensitive.

Representatives for Mr. Trump and for Paramount are involved in settlement talks, and mediation is expected to start this week.

Mr. Pelley’s on-air monologue on Sunday night evoked a previous moment of public discord between “60 Minutes” and its corporate overseers.

In 1995, also in a closing note to viewers, the correspondent Mike Wallace said on air that the program had chosen not to broadcast an interview with a former tobacco industry executive because managers at CBS News had given in to legal pressure. “60 Minutes” ultimately aired the interview, and the episode was later dramatized in “The Insider,” a 1999 movie starring Al Pacino as Lowell Bergman, a “60 Minutes” producer.

Sunday’s “60 Minutes” episode also featured a segment that examined the Trump administration’s decision to reduce funding to the National Institutes of Health, including an interview with a former director who expressed his concerns about adverse effects on Americans’ health.