The Federal Communications Commission is turning its sights on another legacy broadcaster, NBC, as the Trump administration seeks to rein in media companies it characterizes as bad actors that are abusing their privilege of broadcasting over lucrative public airwaves.

The FCC on Tuesday sent a letter to the head, Brian Roberts, of NBCUniversal’s parent company, Comcast, informing him that the agency is investigating the broadcaster’s treatment of local stations it either owns or is affiliated with. 

The letter reads, “For years, the FCC has stepped away from enforcing critical regulations designed to protect localism.”

“This retreat has encouraged large national programmers like Comcast to exert more control over licensed local broadcast stations, eroding the ability of local media to serve their communities,” the letter said. “This has created a clear tension between the many local broadcast stations across the country that want to serve their local communities and the interest of national programmers.”

The letter also said that the chairman of the FCC, Brendan Carr, has heard complaints from local stations that the national networks are using contract negotiations to “extract onerous financial and operational concessions” from local stations and threatening the “termination of long-held affiliations, which could result in blackouts and other harms to local consumers of broadcast news.”

Mr. Carr said the complaints “suggest that the relationships between programming networks and their affiliates are not operating in the manner envisioned by FCC regulations.”

NBCUniversal responded to the letter in a statement, saying, “We have received an inquiry from the FCC and will cooperate with them to answer their questions. We are proud that for many decades we have supported local broadcast TV stations with world-class sports and entertainment, enabling them to drive viewership in a media environment that has grown increasingly competitive.” 

Over the weekend, President Trump — who was one of NBC’s biggest stars for many years as host of “The Apprentice” — posted two messages targeting NBCUniversal, which, for now, owns a left-wing cable network, MSNBC. The cable network is set to be spun off from Comcast as part of a new company, Versant, later this year. Reliably liberal NBC News, however, which has worked arm in arm with MSNBC for almost three decades, will remain in the Comcast fold. Mr. Trump has of late been more vocal about his displeasure with NBC News — and its far-left Washington correspondent,  Yamiche Alcindor — than with overtly progressive MSNBC.

“Wow, ‘Concast’s’ NBC is down in viewership almost 28% this year. Their programming is terrible, their management even worse. They are an arm of the Democrat Party, and should be held accountable for that,” he said in a post on Truth Social. 

In another post, he suggested the FCC should revoke NBC’s broadcast license. 

Mr. Trump had a falling out with NBC in 2016 when, after he’d left the show to run for president, NBC’s then entertainment chairman, Robert Greenblatt, said Mr. Trump would “never be back on ‘Celebrity Apprentice’ as long as I’m here.” This was after Mr. Trump’s comments about immigration, still novel, had roiled liberal Hollywood, whose denizens never imagined he would actually be elected president. 

The rift between Mr. Trump and NBC deepened when he assumed office and was annoyed by how NBC News and its sister news operation, MSNBC, covered his White House. Ms. Alcindor, who in Mr. Trump’s first term was also working for far-left PBS, would challenge him repeatedly with opinionated questions.

Eight years later, with the second Trump term well under way, Mr. Carr has vowed to “constrain” national networks and their relationships with local stations. In May, Mr. Carr told CNBC’s David Faber that he has heard complaints from local stations about the broadcast network’s contracts with them. 

“I hear directly from local broadcasters [who] say, ‘Look, I’d like to do something different. I’d like to serve the needs of my local community. I’d like more localism, but I have to take this national program’ in cases where they don’t even want to,” he told Mr. Faber.

While Mr. Carr has spoken about how he feels there is a need to reform regulations to support local stations and limit national networks, the investigation comes as he has embarked on a mission to use the regulatory authority of his agency to call to account the major broadcast networks — ABC, NBC, and CBS — which have long been accused of a liberal bias. These “big three” networks have proprietary access to public airwaves, which are a gateway to enormous profits, and the networks are legally obligated to produce fair and unbiased news coverage.

Under Mr. Carr’s leadership, the FCC has used a variety of methods to try to force the networks to make changes to their policies and even coverage. Mr. Carr has tried to force companies to abandon diversity, equity, and inclusion initiatives by threatening to block mergers of companies that have them. He has also launched investigations into ABC, its parent company, Disney, and Comcast over their diversity policies.

Perhaps the most notable recent example of the FCC using its authority to force companies to pledge to abandon left-wing policies and commit to unbiased journalism is what happened with CBS News and its parent company, Paramount Global, which had its merger with Skydance Media delayed for months as Mr. Trump sued the network for $20 billion.

After Paramount’s July 1 announcement that it would pay $16 million to settle Mr. Trump’s lawsuit, Skydance executives met with the FCC and laid out their commitments to unbiased journalism and airing diverse viewpoints, as well as to eliminate diversity initiatives.

Left-wing legal scholars and reporters largely cast the delay in the merger as Mr. Carr using his authority to pressure Paramount to pay Mr. Trump and bend CBS to the administration’s will. Mr. Carr and Paramount have both said Mr. Trump’s lawsuit was unrelated to the Skydance deal. Mr. Carr also said Skydance’s commitments to unbiased journalism were what paved the way for the FCC to approve the deal. 

The troubles for CBS might not be over, as Mr. Carr said that the FCC is still conducting a news distortion complaint related to the editing of Vice President Harris’s interview with “60 Minutes.”

The FCC has rarely revoked broadcast licences, though Mr. Carr has suggested the agency should consider taking the step, but the investigation into NBCUniversal and its contracts with affiliates could result in fines or other conditions to punish the network.