A 40-year-old Maine man wanted on sexual assault charges was shot and killed by Massachusetts State Police troopers across the border in New Hampshire late Thursday as a nearly hour-long pursuit that began in Malden came to a fatal end, officials said.

Michael R. Brown was wanted on charges in his hometown of Presque Isle, Maine, and was the subject of an alert to New England law enforcement that he was armed with a stolen handgun, officials said Friday.

Brown’s sister, Colleen Brown, said her brother had been missing since June 7 and that the family feared he might have harmed himself. She also said that her brother had been in trouble with the law since he was 16 years old, and “doesn’t know how to keep his hands off women.’’

“We didn’t know if he was dead or alive,’’ Brown, 36, said in a telephone interview Friday. “We were worried. ... We didn’t want him out there hurting anybody else.’’

The last time she saw her brother was last week, when she heard a noise outside her home. She looked outside and saw him dive in front of a lawn mower, in an attempt to hide.

Given the way he was acting, Brown figured he was high on drugs and looking to see if keys were left inside her vehicle. Brown locked her door and called the police. “He was mentally unstable,’’ she said.

Looking back, she wishes that her brother got the help that he needed, and that his cohorts had cooperated more with the police, instead of helping him when the police were looking for him.

“When they’re not in their right mind, they don’t know what’s best,’’ she said. “He didn’t turn to us. If somebody had been talking to him, if someone could have reached out to him, maybe things would have been a little different. That’s hard to deal with.’’

“I think a lot of this could have been prevented.’’

According to authorities in both states, around 11:10 p.m. Thursday, Brown was spotted in Malden, where that city’s police tried to pull him over in the 400 block of Eastern Avenue. Brown drove off, leading State Police through multiple towns during which he allegedly opened fire on troopers and drove for some distance in the wrong direction on Interstate 495 in Amesbury.

Stop sticks were deployed by police during the pursuit, damaging the tires on the vehicle Brown was driving, but he continued to avoid police until he arrived in Newton, N.H., and crashed into a tree, officials said.

The crash occurred around 11:51 p.m. Thursday.

At that point, Massachusetts troopers confronted Brown, New Hampshire Assistant Attorney General Jeffrey Strelzin told reporters Friday. The New Hampshire state medical examiner conducted an autopsy and concluded Brown died from a gunshot to the neck, not from a self-inflicted wound, officials said.

“There was a confrontation [at the crash site] and the suspect was shot and killed,’’ Strelzin said. “We believe it happened very quickly.’’

He said a stolen handgun was found inside the wrecked vehicle that Brown was driving.

“But without doing further work on the case, I cannot tell you whether or not it was fired’’ at the final confrontation, Strelzin said.

Strelzin said the Massachusetts troopers surrendered their department-issued firearms to New Hampshire authorities as part of the investigation. He said the troopers will likely be interviewed next week.

According to Massachusetts State Police spokesman David Procopio, several troopers involved in the case have been placed on administrative leave with pay while the investigation is ongoing.

Emily Sweeney can be reached at esweeney@globe.com. Follow her on Twitter @emilysweeney. John R. Ellement can be reached at ellement@globe.com. Follow him on Twitter @JREbosglobe.