A former reporter for a news website was charged on Friday with making more than a half-dozen bomb threats against Jewish community centers, schools and a Jewish history museum, federal authorities said.

The man, Juan Thompson, 31, of St. Louis, made some of the threats using his own name and others implicating a former girlfriend as part of an effort to intimidate her, the authorities said in a federal complaint unsealed on Friday in Federal District Court in Manhattan.

In one threat, made on Feb. 1 against a Jewish school in Farmington Hills, Mich., the complaint says, Mr. Thompson claimed he had placed two bombs in the school and was “eager for Jewish newtown,” an apparent reference to the 2012 school massacre in Newtown, Conn., in which a gunman killed 20 students and six school employees.

The website The Intercept confirmed in a statement on Friday that Mr. Thompson worked for the publication for a little more than a year, until he was fired in January 2016 after it was discovered that he had fabricated sources and quotes in his articles.

The arrest came amid heightened tension involving more than 100 threats against Jewish groups that have been reported in dozens of states this year, resulting in a broad inquiry led by the Federal Bureau of Investigation. The threats, combined with vandalism at Jewish cemeteries, have prompted fears of an increase in anti-Semitism.

Mr. Thompson is not believed to be responsible for most of the threats against Jewish centers around the country, according to federal law enforcement officials who spoke on the condition of anonymity because the investigation was continuing.

Investigators are still trying to identify who is responsible for those threats, which the officials said were made using sophisticated technology to mask personal details, like identity and the origin of the internet-based calls.

The federal complaint, which was signed by Christopher Mills, an F.B.I. special agent, says Mr. Thompson’s threats were “part of a sustained campaign to harass and intimidate” the former girlfriend. The harassment began shortly after she ended their romantic relationship last July, the complaint says.

Mr. Thompson made at least eight threats against Jewish schools and community centers in New York, Dallas, Farmington Hills and San Diego, according to the complaint.

In a threat made on Feb. 22 to the Anti-Defamation League in New York, the complaint says, a caller, using an untraceable phone number and a tool that disguised the caller’s voice, said there was C-4, an explosive material, in the group’s New York office, and that it would be “detonated within one hour.” The office was immediately searched and no explosives were found.

The accusations against Mr. Thompson were announced on Friday by Preet Bharara, the United States attorney in Manhattan; William F. Sweeney Jr., head of the F.B.I.’s New York office; and James P. O’Neill, the New York police commissioner.

“Threats of violence targeting people and places based on religion or race — whatever the motivation — are unacceptable, un-American and criminal,” Mr. Bharara said in a statement. “We are committed to pursuing and prosecuting those who foment fear and hate through such criminal threats.”

The F.B.I. said that its director, James B. Comey, and top bureau officials had held a meeting on Friday with Jewish community leaders to discuss the recent increase in threats to Jewish institutions around the country, and that the investigation into the threats was “a top priority.”

Mr. Thompson was arrested on Friday in St. Louis, where a federal magistrate judge ordered him held without bond pending a detention hearing on Wednesday. Mr. Bharara’s office will seek to have Mr. Thompson, who is charged with one count of cyberstalking, brought to Manhattan to face prosecution, an office spokeswoman said.

Lucille G. Liggett, a federal public defender who represented Mr. Thompson in court on Friday, declined to comment when reached later in the day.

Mr. Thompson worked at The Intercept from November 2014 to January 2016, when he was dismissed, according to a statement by Betsy Reed, the news organization’s editor in chief.

In the statement, Ms. Reed said the organization was “horrified to learn” of Mr. Thompson’s arrest in connection with the bomb threats and cyberstalking allegations. “These actions are heinous and should be fully investigated and prosecuted,” she said.

Mr. Thompson began making bomb threats in January after harassing his former girlfriend for several months, according to the complaint. She obtained a New York State order of protection against him last August; it was renewed in October and again in December.

As part of the harassment, Mr. Thompson, without using his actual name, had sent emails and faxes to the woman’s employer that made false allegations about her, including that she was anti-Semitic, according to the complaint. He also sent her an anonymous email, attaching nude photographs of her and threatening to release them publicly.

The bomb threat against a Jewish history museum in Manhattan, which the authorities did not identify, was made on Jan. 28, the complaint says.

The phone threat against the Anti-Defamation League on Feb. 22 was preceded a day earlier by an email to the organization that said that the former girlfriend was “behind the bomb threats against jews” and that she would be making more threats.

At a news conference on Friday in New York, Oren Segal, director of the Anti-Defamation League’s Center on Extremism, said Mr. Thompson had been on the organization’s radar since he was fired for fabricating quotes in articles.

“While the motive is unclear, the impact is crystal clear,” Mr. Segal said of the bomb threats Mr. Thompson is accused of making. “While I cannot speak about what is in Thompson’s mind or certainly in his heart, threatening Jewish institutions is an anti-Semitic act.”