Officers are still pursuing fugitive David Sweat but Cuomo said there was nothing to confirm his location as of Friday night. Still, "several leads" were being pursued on his whereabouts, the governor said.
The search involving about 1,100 officers has transformed life in sleepy hamlets and towns shadowed by the Adirondack Mountains.
For three tense weeks, residents have coped with incessant rumors, constant roadblocks, the buzz of helicopters, state troopers in the schools and homes under lockdown as authorities have pursued more than 2,000 tips into the escapees' whereabouts.
Law enforcement finally closed in on Matt around 1:30 p.m. when police received a call of shots fired near Route 30 in the vicinity of Malone, New York, according to law enforcement officials briefed on the matter. About 20 minutes later, more gunshots were heard.
The driver of a recreational vehicle called 911 when he heard the initial shots. He kept driving and called 911 a second time when he realized his camper was hit, the officials said.
Investigators traced the site of the initial gunshots to about eight miles back from where the driver stopped and discovered the bullet hole in the back of his camper. Officers came upon a cabin where they smelled gunpowder, as if a weapon recently had been fired, New York State Police Superintendent Joseph D'Amico said.
D'Amico said federal officers searching the area heard coughs in the woods. Moments later, Matt -- armed with a 20-gauge shotgun -- was confronted and fatally shot by a Border Patrol tactical team.
D'Amico said Matt, who turned 49 on Thursday, was shot after failing to comply with verbal commands to put his hands up.
"You never want to see anyone lose their life," Cuomo said. "But I would remind people that Mr. Matt was an escaped murderer from a state prison. Mr. Matt killed two people who we know about. Mr. Matt killed his boss in a dispute and dismembered him. He fled to Mexico and then he killed another person in Mexico and was imprisoned in Mexico."
Two sets of footprints were found in the area, the law enforcement officials said. The second set is believed to belong to Sweat.
"We have no actual sighting of Sweat by law enforcement," D'Amico said. "But we have no indication that Sweat wasn't accompanying Matt at the time that he was shot and killed."
The search for Sweat was unfolding around Elephant Head, northwest of Lake Titus and about 10 miles from Malone, according to Clinton County Sheriff David Favro.
At a command center near the Clinton Correctional Facility in Dannemora, New York, law enforcement helicopters were taking off to join the search. Passing motorists honked in approval at news of Matt's death. As nightfall approached, authorities moved floodlights into the area.
"This is definitely the hardest perimeter that I've seen around any area since this manhunt started," Favro said.
Matt's shooting occurred on a day the New York State Police reported that Matt and Sweat might have been headed to Canada. The area where Matt was killed is about 70 miles from Canada.
A reported burglary led police to a cabin on Thursday in Malone, State Police spokesman Beau Duffy told CNN. Malone is about 14 miles northwest of Mountain View, where another cabin was burglarized.
Evidence found in the Malone cabin was being tested, Duffy added. At the time, the fugitives had not been seen, but officers were "certain that the evidence is conclusive," State Police Maj. Charles Guess said Friday at a news conference.
Two prison employees have been charged in connection with the men's elaborate June 6 breakout, and the accusations against them highlight a series of apparent security lapses
Investigators from the New York State Inspector General's Office are looking into possible breaches of security protocols that allowed Matt and Sweat
to escape, setting police on a vast and costly manhunt
for the past three weeks.
Other agencies are conducting investigations at the prison.
Hundreds search dense woods
As the investigations into shortcomings at Clinton continued, hundreds of law enforcement officers had been searching for Sweat and Matt in a densely wooded area roughly 20 miles west of the prison.
Searchers also had been combing the thick vegetation in the area surrounding the Mountain View cabin the escapees were thought to have burglarized.
Matt and Sweat, 35, are both convicted murderers.
Matt was accused of killing a man after a dispute over money, snapping his victim's neck and then dismembering the body.
Sweat is serving a life sentence for the killing of a sheriff's deputy in 2002.
Sweat and another man robbed a gun store and fatally shot the deputy after he confronted them.