Fire and Emergency New Zealand (FENZ) was called to deal with the fire at about 10:45am.
Eleven fire appliances were sent to the scene, with ship engineers joining firefighters onboard the vessel to bring the blaze under control. Fire crews were also stationed dockside to cool the sides of the ship with water.
FENZ has since announced that as of 1:30pm, the fire had been fully extinguished.
FENZ earlier said police had been evacuating pedestrians in the area, with people told to stay away or stay indoors as emergency services worked to extinguish the blaze.
Police had closed the roads surrounding the wharf.
A Napier Port spokesperson told Newshub the situation was being managed.
"The crew, who are currently within their 14 days isolation, have been transferred to another separate facility on port," they said. "Everyone is safe and accounted for."
Footage from the scene filmed by a port worker shows thick black billowing out of the middle of a large ship and being swept by the wind across the harbour.
"There is a lot of smoke around," FENZ added.
"People in properties nearby the Port should keep their windows closed and stay inside due to the smoke. Contact Healthline on 0800 611 116 if you need medical advice."
The vessel on fire is believed to be the Kota Bahagia, a container ship built in 2011 that sails under the flag of Singapore. It's not yet known what cargo was onboard the ship when the blaze broke out.