Police say several shots were fired during an incident at a park in Palmerston on Tuesday morning.
Two officers had gone to the area where it's alleged they found a man armed with a weapon.
"They called upon that person to drop the weapon and unfortunately a number of shots were fired by police, injuring a male," Northern Territory Assistant Commissioner Michael White said.
"He has since been conveyed to Darwin hospital and is currently under treatment in surgery."
Mr White said an investigation had been launched, including the reasons why the man was armed and the circumstances of the shooting.
It will check on possible links to a domestic violence incident earlier in the day in which another person was injured and taken to hospital and also consider the use of force by police, including what other options were used or considered.
"Use of force is something police have to do, it's not something that we want to do," Mr White said.
"We don't come to work every day thinking that we will injure someone or be involved in a police shooting.
"At this time we are certainly making sure that all people involved in this are being provided with the support that they need."
Investigators will liaise with the injured man's family and the wider Indigenous community.
They are also working with a school nearby to ensure all students get home safely and are not impacted by ongoing activity at the crime scene.
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