The incident happened about 8pm while the crews were at work on the log ship Nord Yilan.
Fire crews and St John Ambulance paramedics were called to the scene after it is understood a turbo system on the engine of a digger-loader failed and billowed exhaust smoke through the hold area.
A fire service spokesman said the turbo unit on the engine blew and billowed exhaust fumes, causing the workers in the hold to be affected.
Other port workers were able to remove the digger from the hold before the fire service arrived.
It is understood the digger may have briefly caught fire but was out by the time fire crews arrived.
There had been no fire danger to the ship and the fire crews left the scene just after 9.30pm.
Firefighters in full breathing protection gear had checked the hold to make sure the carbon monoxide had dissipated and helped paramedics treat the affected workers.
The Nord Yilan was scheduled to depart port around 7am on Wednesday.
Napier Port Culture and Capability manager Viv Bull said the management's thoughts were with those who had been affected by the gases.
"We are disappointed that an incident has happened on our port," Bull said.
"As the landowner, Napier Port takes a strong interest in the safe practice of companies operating on our site."
More than five Fire Emergency New Zealand crews attended the blaze at 8pm.