On January 28, 2023, the Kaitaki was sailing into Wellington Harbour when it lost propulsion with more than 880 people on board - resulting in a mayday call.
The ship regained limited power and made its way to port where its passengers were able to safely leave it and come ashore.
This week Maritime NZ filed one charge under the Health and Safety at Work Act following a near year-long investigation into the incident.
The maximum penalty is a fine of up to $1.5 million.
Maritime NZ director Kirstie Hewlett explained the evidence they had investigated.
"It involved reviewing the operator's organisational information relevant to processes and procedures connected to safety and maintenance management, undertaking interviews and examining the Kaitaki after the incident occurred."
Hewlett said evidence was comprehensively reviewed before the decision was made to prosecute.
She said Maritime NZ cannot make any further comment about the ongoing proceedings due to it being before the court.
KiwiRail chief executive Peter Reidy said passenger and staff safety will always be their highest priority.
"The safe and reliable operation of the Interislander service is an absolutely non-negotiable requirement for KiwiRail board and management.
"Following the Kaitaki incident, we conducted a full review of all of our asset management practices, using global experts to ensure we are running the Interislander to world's best practice standards."
He said they were pleased the Interislander ferries had operated with 100 per cent asset reliability and 91.4 per cent on-time performance over the recent busy Christmas period.
