At the time of the accident, several contractors were at work on the vessel, with the hatch on the main deck left vented, or partly open, to allow hoses and cables to pass through it.
In his judgment, District Court Judge Ian Mill said the company "either foresaw the risk but did not take all reasonably practical steps in the circumstances of this case or ought to have foreseen the risk and failed to do so".
"These practical steps were no more than ones already available but not used because the captain and crew were lulled into a false sense of security from years of using the same practice without incident and always treating a vented hatch as safe," Judge Mill said.
Maritime NZ director Keith Manch said lessons must be learned from the incident.
"This was a tragic incident that could have been avoided through very simple measures," he said.
"Ships are inherently dangerous working environments and employers must ensure all practicable safety steps are taken to protect their employees when they are on the job. All employees have the right to come home safely from work.
"Our thoughts are very much with the family of Cain Adams, for whom this case will have been extremely difficult, but the whole of the maritime sector must heed the lessons of this case."
The maximum penalty for the charge is a fine of $250,000.
