The crewman fell unconscious and was rescued by Fire and Emergency New Zealand.
He was taken to Tauranga Hospital where he was placed in an induced coma. He was discharged from hospital on September 10 and has made a full recovery.
The Maritime NZ investigation established that the vessel had been fumigated before departing Malaysia where the cargo was loaded.
It included using the chemicals aluminium phosphide and ammonium carbonate, which can produce toxic gases phosphine, hydrogen phosphine, ammonia and carbon dioxide.
When the ship arrived in Tauranga, the holds were opened and tested by an approved testing agency to ensure there were no traces of phosphine gas.
But the agency failed to test for concentrations of oxygen in the holds.
About 4.30pm on September 6, the victim entered the cargo hold to undertake cleaning and blowing operations. A crewmate was with him at the time.
No atmospheric testing of the oxygen levels or other gases in the hold were done.
No entry permit was issued, nor were any hazard identification and risk assessment processes undertaken prior to the crewman's entry.
As the crewman climbed down the hatch ladder into the hold and neared the bottom, he became disoriented and blacked out, falling about 1m to the platform below.
His crewmate raised the alarm.
The victim was unconscious in the hold for about 10 to 15 minutes until local firefighters were safely able to bring him out and he was taken to Tauranga Hospital.
False or misleading information was provided to Maritime NZ by the ship's captain Walter Damian and chief officer Ian Dalingding, the agency said.
This included an enclosed spaces entry permit and a hazards identification and risk assessment form being prepared by Damian after the collapse of the crewman.
The permit falsely stated pre-entry atmospheric testing had been undertaken and further testing done on five other occasions and safety harnesses had been worn by the victim.
Dalingding pleaded guilty to one charge of providing false information.
Damian also pleaded guilty to two charges of providing false or misleading information and permitting an activity which endangered or risked the safety of the crew member.
Sentencing Judge Denys Barry said the risk to the victim was significant.
"When the victim crewman entered the narrow booby hatch ladder, the hazard and risk were high. If he had lost consciousness higher up, he could have been badly injured or killed," the judge said.
Damian was fined $13,500 and Dalingding $4050, plus a $10,000 emotional harm payment was awarded to the victim.
Maritime NZ said oxygen depletion and gas build-up in a ship's hold was "an internationally known risk" and a major concern for the agency.
"International law required shipping operators to have a safety management system including ensuring entry to enclosed spaces such as cargo holds were always risk assessed and effectively managed," the agency said.
Maritime NZ said as well as taking the prosecution, it had shared details of the incident and this ship with other Asia-Pacific countries' maritime authorities.
The matter has also been reported to the Isle of Man registry,
