The 45-year-old suspect, who was known to the police, was arrested an hour after the first shots were reported at about 18:00 local time (08:30 GMT).
Police said they believed the man had acted alone. The crime scenes reportedly included a motel and a bar.
Prime Minister Scott Morrison said the shooting was not terror-related.
Mass shootings in Australia have been a rare occurrence since the country overhauled its gun laws in 1996, in the wake of a shooting in Tasmania that left 35 dead.
The alleged gunman, who had been on parole since January, was wearing an electronic tag, Northern Territory Police Commissioner Reece Kershaw said.
"We're still trying to establish the intent and motivation behind this," he told journalists.
The gunman was reportedly carrying a pump action shotgun, and up to 20 gunshots were heard.
Eyewitnesses said the gunman entered the Palms Hotel in the suburb of Woolner and opened fire in a number of rooms before fleeing. One person was reportedly killed there while a woman was wounded.
"A man came running with a woman in his arms from next door which is the Palms Motel, which is the motel next to my motel, and he just dropped her on the footpath right in front of us," a witness, Leah Potter, told ABC News
"I ran and got some towels and wrapped up her legs, she had little holes all in her skin on both her legs and she was bleeding everywhere."
Another witness, John Rose, told ABC that he saw the gunman walk into the motel with a sawn-off shotgun.
"He shot up all the rooms and he went to every room looking for somebody and he shot them all up, then we saw him rush out, jump into his Toyota pick-up, and rush off," Mr Rose said.
The suspect then travelled to four other locations, according to the Sydney Morning Herald, including the Peter Macauley Center - a police operations base.
Another person was killed at Buff Club, another at Gardens Hill Crescent and another at Jolly Street, according to the newspaper.