The White House directed Kash Patel, the F.B.I. director, to oversee a leak investigation into reporting by The New York Times about security issues with the new Air Force One, leading to a flurry of subpoenas to several Times reporters Friday night, according to people with knowledge of the situation.

Mr. Patel scuttled a planned trip to Chicago and spent roughly eight hours at the White House on Friday, running the investigation from there rather than F.B.I. headquarters — a major departure from historical practice. Mr. Patel also briefed senior administration officials on the investigation, two people said. The people spoke on the condition of anonymity to describe sensitive internal discussions.

The White House’s deep involvement in the case came after officials said that President Trump was enraged about the coverage of the Qatari-donated plane, which The Times reported Thursday lacks the same defensive countermeasures of the previous Air Force One.

Mr. Trump flew on the new jet to a NATO meeting in Turkey earlier in the week, but was forced to change to the old plane when he departed because of Secret Service concerns, as The Times reported on Wednesday.

Mr. Patel’s role in the investigation, in close coordination with top administration officials, reflects a further dismantling of the wall that had separated the White House and the F.B.I. in previous administrations. The government’s effort to immediately seek information from journalists, when such cases are typically centered first on identifying potential internal wrongdoing by officials, comes as the Trump administration has intensified pressure on news organizations.

In response to a request for comment, Steven Cheung, the White House communications director, said that “President Trump is laser focused on helping the American people and keeping them safe. That will always be his priority.”

Emily Covington, the director of the Justice Department’s Office of Public Affairs, sought to downplay the unusual nature of the subpoenas, some of which were delivered late Friday night directly to the doors of the reporters’s homes.

“Every administration has addressed the crime of leaking national security information,” she said in a statement. “To the extent that we have to investigate breaches of national security, that’s something that we will continue to do.”

She added: “To be clear, reporters are not the targets. Those leaking classified information are.”

Ben Williamson, an F.B.I. spokesman, said in a statement that “Director Patel and White House officials agreed to meet on Friday at the White House to brief an ongoing matter. While we would not comment further, other speculative reporting regarding the nature of the meeting is absolutely false.”

One person briefed on the conversations said that Mr. Patel had his own concerns about the type of information publicly disclosed about the plane. Another person said that Mr. Patel went to the White House on his own volition to oversee the investigation.

Mr. Trump had sought the rapid retrofitting of the Qatari-donated 747 after he learned that two new Boeing planes that were supposed to replace the aging ones used as presidential aircraft would be delayed for years.

Mr. Trump has basked in the luxury of the new plane, which is more than a decade old but has the kind of opulent furnishings the president prefers. He has repeatedly described the Qatari jet as cost free to the United States. But in reality, hundreds of millions of taxpayer dollars were spent to upgrade its security systems. Officials have said that he plans to take the plane with him as a donation to his presidential library when he leaves office.

While Mr. Trump has said the Qatari plane was upgraded with the necessary security “bells and whistles,” The Times reported on Thursday that it lacks the defensive countermeasures that were security features of the old model, including its advanced antimissile capabilities.

Experts said the absence of the capabilities creates a potential risk when Air Force One is flying overseas, not only for the president, but also for the large entourage of White House staff members, Secret Service officials, journalists and guests who fly aboard.

After the Secret Service urged him to fly the old Air Force One out of Ankara, Mr. Trump announced that he was making a swap in aircraft. In a post on social media, he claimed that he was taking the older plane to the United Kingdom for “old time’s sake,” and that he wanted to show the new jet to U.S. troops on a military base there.

Once he landed at Mildenhall Air Force Base in England, he walked from the older plane to the Qatari-donated jet, which transported him back to the United States.

When The Times and other news organizations began reporting this week on the security issues with the new plane, the president was livid, according to an official with knowledge of his comments who was not authorized to discuss the matter publicly.

Before The Times’s first article was published, a senior official at the F.B.I. contacted a reporter and a senior editor to ask that the article be held, calling it an issue of national security. The F.B.I. official declined to explain the security issue. The official also asked The Times to disclose its sources for the article. The newspaper refused to do so.

On Friday, after Mr. Patel left the White House, he posted a message on social media confirming that he had been there, and said that “the fake news will find out why soon.”

That night, 48 hours after The Times had published the first article on the new plane, its reporters were served with subpoenas demanding that they provide evidence before a grand jury on July 15.

In a statement, David McCraw, The Times’s top newsroom lawyer, said, “This brazen act should be seen as nothing more than an attempt to prevent the public from knowing what is happening in their country by intimidating journalists from doing their jobs.”

The rapid escalation of the case is a sharp departure from past national security leak investigations. Typically, officials first seek to establish how many people have had access to the information that was made public. Depending on the size of that group, prosecutors then attempt to determine ways to eliminate potential suspects from the list. In past leak cases, such efforts have often been abandoned if the pool of potential leakers is simply too large to scrutinize.

Historically, the Justice Department has sought to subpoena reporters only as a last resort after other reasonable options have been exhausted.

The Trump administration has pushed for a number of leak investigations, several of which have been conducted by federal prosecutors in the Eastern District of Virginia. Those efforts, which included subpoenas to reporters from The Wall Street Journal and The Washington Post, foundered in the face of resistance from a federal judge, according to multiple people familiar with the matter. Federal prosecutors withdrew them last month.

The subpoenas issued to Times reporters on Friday were from a different jurisdiction, the Southern District of New York, and were sought by Jay Clayton, the U.S. attorney in Manhattan, who was recently nominated by Mr. Trump to serve as the director of national intelligence.

The subpoenas seek the reporters’s testimony on the same day Mr. Clayton is set to face a Senate confirmation hearing for his new post. The same day, Todd Blanche, the acting attorney general, is set to take part in a confirmation hearing to serve as attorney general on a permanent basis.