The FBI began investigating a New York Times reporter after the newspaper published a story raising concerns about the security arrangements surrounding the girlfriend of Kash Patel, the FBI director, the Times has reported.

According to reporting from the Times on Wednesday, the inquiry into Elizabeth Williamson, the reporter, began in March following an article she reported alleging that Patel used FBI resources to provide protection and transportation for his girlfriend, the country singer Alexis Wilkins.

The report, citing a source familiar with the matter, states that FBI agents searched databases for details about Williamson, and suggested further steps to assess whether her actions might violate federal stalking laws.

Patel denied the investigation during a Wednesday appearance on Fox News with Sean Hannity, the host, who raised the issue while referencing his own disputes with the Times, including that he considered legal action over previous coverage about his views on Covid-19.

“The reality is … that this same reporter delivered a baseless story which caused a direct threat of life to my girlfriend,” the FBI director told the host. “We’re going to protect not only me and my loved ones, but every American that is threatened.”

Joseph Kahn, executive editor of the Times, criticized the FBI’s actions, arguing that investigating a journalist for standard reporting is inappropriate.

“The FBI’s attempt to criminalize routine reporting is a blatant violation of Elizabeth’s First Amendment rights and another attempt by this administration to prevent journalists from scrutinizing its actions,” Kahn said in a statement published by the Times. “It’s alarming. It’s unconstitutional. And it’s wrong.”

The original piece, published on 28 February, examined the use of federal officials assigned to perform personal duties for an administration figure. Williamson wrote that Patel had assigned four agents to protect Wilkins full time, and that they had transported her to appearances in Britain, Illinois and Nashville.

The FBI, in its own statement to the Times, said that “while investigators were concerned about how the aggressive reporting techniques crossed lines of stalking”, it was not moving forward with a case against Williamson.

The FBI did not immediately respond to the Guardian’s request for comment.

Earlier this week, Patel carried out a previous threat to sue the Atlantic and Sarah Fitzpatrick, a journalist, over an article that included claims of “excessive drinking” and “conspicuous inebriation and unexplained absences” during his leadership of the FBI.

The Atlantic’s report cited “six current and former officials and others familiar with Patel’s schedule”, stating that early in his tenure, “meetings and briefings had to be rescheduled for later in the day as a result of his alcohol-fueled nights”.

The lawsuit, filed in US district court for the District of Columbia, seeks $250m in damages. Patel’s attorneys described the article as “a sweeping, malicious and defamatory hit piece”.