The father of a missing New Hampshire girl who was last seen over two years ago has been arrested in connection to the case, police said.

The Manchester Police Department first reached out to the public for tips on the whereabouts of 7-year-old Harmony Montgomery last week, after it learned she had not been seen since late 2019.

Adam Montgomery, 31, was arrested Tuesday on charges including felony second-degree assault “arising from 2019 conduct against Harmony Montgomery,” police said.

Montgomery also was charged with interference with custody and two charges of endangering the welfare of a child, both misdemeanors. Montgomery has legal custody of Harmony but has not had her in his physical custody since approximately November 2019, according to the complaint.

Montgomery waived his right to an arraignment hearing at the Hillsborough Superior Court Wednesday and agreed to be placed in preventive detention, according to court records. ABC News reached out to his attorney for comment.

According to an affidavit released Wednesday, family members told police they were concerned Montgomery was putting Harmony in physical harm. Montgomery allegedly told his brother that he gave Harmony a black eye and “bashed her around his house,” the affidavit stated. The brother notified the state’s Division of Children, Youth and Families about the injury after he saw Harmony with a black eye in July 2019, according to the affidavit.

Harmony’s mother told authorities she believes she last saw her daughter around Easter 2019 in a FaceTime video call, during which the girl “seemed frightened,” according to the affidavit.

Her mother lost custody of Harmony in July 2018 in part due to a substance abuse issue and has since regained sobriety, according to the affidavit. She contacted Manchester police in November after she was repeatedly unable to find Harmony or her father, the affidavit said. The department launched an investigation after the state’s Division of Children, Youth and Families notified police on Dec. 27 that the agency had been unable to find Harmony, according to the affidavit.

Police interviewed several family members to try to determine the last time Harmony was last seen. Montgomery’s current wife told police she last saw the girl in November or December 2019 with her father, who allegedly told her he was driving Harmony to her mother’s in Massachusetts, according to the affidavit. His wife “never saw, or heard about [Harmony] after that day,” and last saw Montgomery in October, the affidavit stated.

Police located Montgomery sleeping in a car in Manchester on Dec. 31, at which point he “made some contradictory comments during our interaction which raised our suspicion and concern for [Harmony’s] well-being,” the affidavit stated. Montgomery allegedly told police he had seen Harmony “somewhat recently,” then said he hadn’t seen her since her mother picked her up in Manchester in November 2019, according to the affidavit.

His girlfriend, who was with him at the time, told police she did not know where Harmony was, according to the affidavit.

The search for Harmony continues, as police are urging anyone with information to contact its dedicated tip line. Manchester Chief Allen Aldenberg told reporters Monday police are assuming she is “alive and well somewhere,” and that he hasn’t seen anything to suggest otherwise yet.

“This is not a recovery,” Aldenberg said during a press briefing. “All efforts are focused on that Harmony is alive, and we are going to do everything we can to find her in that condition.”

Part of the investigation will involve determining why it took over two years for Harmony to be reported missing, he said.

“I want to focus on locating her now and dedicating all of our efforts to that,” the chief said. “If there was some flaw in the system, I’m not saying there was, but if there was, where was it and how’s it going to be addressed?”

Harmony was reunited with her father after spending time in foster care in Massachusetts, ABC Manchester affiliate WMUR reported, citing a source close to the child. New Hampshire Division of Children, Youth and Families officials told WMUR that contact with the family is gradually reduced after reunification.

“It’s difficult to account for what happened when we are not engaged with the family,” Joe Ribsam, the agency’s director, told WMUR. “What’s important to figure out right now is what has been happening with this young girl for the past few years.”

A reward for information leading to Harmony has reached $43,000.

“More than two years have passed since Harmony was last seen,” Aldenberg said. “That puts us at a disadvantage, and the public’s help is greatly needed.”