It's believed the incident began unfolding around 6pm.
A police spokeswoman confirmed the emergency response was sparked by an individual who had "made threats".
A man had now arrested and would front court.
A source who is at the base tonight has contacted the Herald.
"I was on the base at the time and we were told by AF personnel to clear the area," the man said.
"There was a police helicopter, and multiple emergency vehicles.
"Apparently someone had driven a vehicle into a hangar and was making threats about explosives."
The source said there was a strong sense of urgency among air force personnel. People were being allowed to leave but not enter the base.
Police earlier said a man had been taken into custody without incident and was speaking with police.
Emergency services responded to the base earlier this evening where the male had made threats.
Cordons remain in place at roads leading to the base until further notice, police said.
Auckland Transport is advising members of the public to avoid the area.
The police media event publisher describes the incident as a "bomb scare" on Tainui Cres, Whenuapai.
A Herald reporter earlier said a roundabout at the end of State Highway 16 had been blocked off by police, preventing access to the air base from Brigham Creek Rd.
Trig Rd has also been cordoned off by emergency services. A succession of vehicles were earlier pulling up the cordon and being turned away.
A Herald Island resident said she is unable to get home tonight due to police cordons.
Whenuapai resident Andrew Head had been blocked from driving back to his home, and told the Herald a police officer had informed him there was a bomb scare at the air base.
Head had been heading back from Westgate with his daughter. He came back to Brigham Creek roundabout, which was blocked off, and could see armed police further up the road.
"I spun about and went up to Trig Rd, but that was blocked off. Then I drove all the way up to Westgate and came down to Brigham Creek and that was blocked of. So we've gone to Kumeu and are having a meal."
He spoke to an armed female police officer who told him of the bomb scare and said to "park up and wait".
Police confirmed the Armed Offenders Squad had been deployed.
"As a precaution, roads leading to the area have been cordoned off, including the Whenuapai motorway off-ramps."
Fire and ambulance services have been approached for comment.
Whenuapai Mini Mart owner Narendra Patel, whose shop is within sight of the air base, could see six or seven police cars with their lights on, blocking the road from outside his shop onward.
Another witness said they saw three fire trucks at the air base and another three coming from the North Shore.
The Herald has sought comment from the New Zealand Defence Force.
