Earlier, police officers could be heard calling out to the man: "Come outside now".
The incident started when a police officer tried to stop a vehicle on Te Awanui Drive about 3.40pm.
The man - the sole occupant in the vehicle - made threats towards the officer before fleeing on foot to the nearby marina, where he immediately got on to a boat moored nearby.
Orca Wild Adventures owner Mark Tucker was cleaning his tour boat yesterday afternoon when the first armed offenders arrived at the Tauranga Bridge Marina.
"It's always scary to see police with firearms," he said.
"We didn't really know what was going, we just saw a lot of police," he said, who told them to stay away and stay safe.
Tucker was concerned that if the incident dragged out he would have needed to cancel tours this morning.
But after arriving at 6am, about an hour after the 13-hour incident ended, it was all cleared.
"Big night for them, eh," he said.