Federal prosecutors in Boston unveiled criminal charges on Friday against three men accused of vandalizing the homes of journalists in New Hampshire and Massachusetts in retaliation for an investigation into a local businessman.

The charges stem from a string of incidents last spring after New Hampshire Public Radio aired an exposé about sexual misconduct allegations against Eric Spofford, who until recently had owned the state’s largest network of drug and alcohol rehabilitation centers. Mr. Spofford later sued the news organization for libel.

Mr. Spofford was not named in the criminal complaint. But a person repeatedly named by prosecutors as “Subject 1” is Mr. Spofford, according to a person familiar with the investigation. The complaint said that a “close personal associate” of Subject 1 “solicited” the three men to attack the homes.

Lauren Chooljian, a senior reporter at the radio station, had a window smashed and her house graffitied. Her editor, Daniel Barrick, was targeted. The home of Ms. Chooljian’s parents was vandalized twice in a month.

The attacks represented an unusually intense assault on a small news organization. Coupled with legal threats against the journalists and their sources by Mr. Spofford, the incidents appeared to be part of a broader pattern of politicians and wealthy individuals going to increasingly extreme lengths to punish journalists for negative coverage.

Last year, the U.S. Press Freedom Tracker identified 41 journalists who were physically assaulted. In one case, a Nevada politician was charged with murdering a reporter investigating him.

“Today’s charges should send a clear message that the Department of Justice will not tolerate harassment or intimidation of journalists,” the acting U.S. attorney for Massachusetts, Joshua S. Levy, said in a statement on Friday. “If you engage in this type of vicious and vindictive behavior you will be held accountable.”

Prosecutors with the U.S. attorney’s office charged the men — Tucker Cockerline, Keenan Saniatan and Michael Waselchuck — with conspiracy to commit interstate stalking. Mr. Cockerline and Mr. Waselchuck were arrested Friday morning; Mr. Saniatan remained at large, prosecutors said. The charges carry a punishment of up to five years in prison.

The person accused of soliciting the attacks, identified in the complaint as “Subject 2,” is a New Hampshire resident who was in frequent phone contact with Subject 1, prosecutors said.

Mr. Spofford and his lawyers did not immediately respond to requests for comment on Friday. The complaint does not say whether Mr. Spofford was aware of the vandalism.

Mr. Spofford has denied the sexual misconduct allegations and said he had nothing to do with the vandalism of the houses, which took place in April and May 2022. In a statement last year, he said that he had many supporters and speculated that “perhaps one of them felt compelled to do these acts in a misguided attempt to defend me.”

After New Hampshire Public Radio published its investigation into Mr. Spofford last spring, Mr. Spofford repeatedly threatened the news organization and some of its sources with litigation. The homes of Ms. Chooljian and her parents were vandalized less than two days after NHPR refused a demand by Mr. Spofford to retract its article.

Mr. Spofford sued NHPR and others in September. A state judge dismissed the case but said Mr. Spofford could file an amended suit, which he has said he intends to do.

The criminal complaint said that the F.B.I. obtained phone and other records that showed the accused men coordinating with Subject 2 around the time of each attack. Location data from their cellphones corresponded with the times and locations of the vandalism.

The man who attacked Ms. Chooljian’s home in Melrose, Mass. — throwing a brick through a window and spray-painting “JUST THE BEGINNING!” in red — was captured on a doorbell camera, wearing a blue raincoat and a backpack.

The complaint included an image of Mr. Waselchuck from a month earlier wearing what appeared to be the same raincoat and backpack. Mr. Waselchuck’s cellphone records also indicated that he was near Ms. Chooljian’s home at the time of the attack.

Lawyers for Mr. Cockerline and Mr. Waselchuck declined to comment. Mr. Saniatan couldn’t immediately be reached on Friday.

“We trust that the justice system will hold the perpetrators accountable,” said Jim Schachter, the chief executive of New Hampshire Public Radio. “Journalists doing their jobs — reporting open-mindedly in the public interest — should not have to worry about threats of violence or attacks on their homes and their families.”

A spokeswoman for the U.S. attorney’s office said the investigation was ongoing.

Kirsten Noyes contributed research.

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