Less than a year after he signed a three-year contract to be Kingston’s top administrator, Jim Thomas has resigned following allegations of threatening behavior against female employees.

Town selectmen last week released a settlement agreement with Thomas in which he agreed to leave the town administrator position last Monday in return for a settlement of more than $47,000.

Selectmen said the money amounted to vacation time owed him plus three months severance pay based on Thomas’s salary of close to $120,000 a year. The town’s settlement of $47,387 is “equivalent to payment for 115.5 hours of vacation leave and 4 months of severance pay,” according to the agreement signed by four of the town’s five selectmen.

Selectmen chairman Joseph Casna Jr. said the agreement was a good result for the town.

“We settled in record time and for a reasonable price for what was actually owed” — the vacation time — plus severance pay that represented only a small part of the value of the remaining time on Thomas’s contract, Casna said. “Once everybody realized what we were doing, we needed to focus on what was best for the town.”

Thomas could not be reached for comment. Attorney Douglas Louison, who represented him in court against allegations of making threats, said the resignation does not imply any wrongdoing on Thomas’s part.

“It’s ‘without cause,’ ” Louison said. “There were never any charges brought against him or allegations of misconduct by his employers, the Board of Selectmen.”

Thomas has been on leave since June 7 following an incident in which he allegedly made a threat against Selectwoman Susan Munford, who is also a Kingston police sergeant.

“Attention came to me of the problems,” Casna said Tuesday. “The decision was made to put Thomas on administrative leave pending action . . . to move forward to discipline or what we might want to do.”

Munford said Tuesday that Thomas developed an animus toward her after she questioned his plan for the town to join the state health care program at a meeting with four town employee unions in which she represented police officers.

“I was more vocal,” she said. “I was the leader.”

She said that Thomas sought to retaliate against her by pressuring the town’s police chief to give her undesirable night shifts.

After that incident, Munford said, she learned through her police duties that four other female town employees said they also had been victims of harassment by Thomas. Munford brought this information to selectmen in January, but, she said, the board failed to look into the complaints.

She then took out papers to run for selectman and was elected to the board in April.

After an incident this spring in which two Town Hall employees allege they overheard Thomas angrily threaten to “bring her [Munford] down,” Munford filed a complaint of criminal harassment against him in Plymouth District Court, and the Board of Selectmen voted to place Thomas on leave.

“I was the last one to give up on him,” said Casna, who acknowledged the board’s action came as a result of Munford’s complaints.

“I liked Thomas,” said Casna, part of the board that hired him to be Kingston’s town administrator last September after Thomas left a similar post in West Warwick, R.I. But Thomas moved too quickly in trying to bring changes to local government, he said. “We hired a stallion and hitched him up to a plow.”

Casna said Thomas possessed the education and the experience needed for the job and “had good ideas.” But “something was missing,” Casna said, in his “dealing with people.”

“Kingston is a small, close-knit town,” Casna said. “It takes a while to blend in.”

Thomas successfully defended himself against Munford’s request for a protection order for criminal harassment when a judge ruled recently that one of three instances of alleged harassment did not meet the legal criteria for criminal harassment. The law requires three instances of “willful and malicious” harassment to grant the order.

Louiston argued in court that Thomas’s behavior amounted to nothing more than raising his voice in bargaining sessions.

“I’m glad the judge did what she did,” Louison said. “It was not the kind of behavior that was needed for the harassment law.”

Munford, however, said that Judge Kathryn Hand warned Thomas that if there were further instances of such behavior, she would grant a restraining order.

Munford application’s for a complaint of criminal harassment (which does not include a restraining order) is still before the district court. It was scheduled for a “show cause” hearing, but the hearing was postponed to allow the court to bring in a judge from a different district to prevent any appearance of favoritism because Munford often represents Kingston in Plymouth District Court.

Munford has also filed complaints of unfair labor practice and open meeting violations against Thomas that are still pending.

Casna said he’s in no hurry for the board to hire a new town administrator. Summer is a slower time for town business, he said, and the town can get along without a new chief administrator for a while.