This story has been updated to clarify the Aratere will arrive in Picton on Sunday and the order had not yet been placed.
The stricken Aratere will immediately be placed under a detention order when it gets back to Picton, barring it from movement due to safety concerns.
The Interislander ferry ran aground 3km north of Picton on Friday night with eight specialist drivers and 39 crew on board.
It was refloated on Saturday night on the high tide, and will be towed to Picton Harbour for re-ballasting and stabilising Sunday.
Maritime NZ director Kirstie Hewlett said it will be placed under a detention order upon its arrival in Picton.
"This will enable Maritime NZ to work closely with Aratere's Classification Society and KiwiRail to understand what has occurred, and what action needs to happen, before the vessel is able to move safely again and can be released."
Maritime NZ investigators would start an investigation into the grounding on Sunday, she said.
"They will carry out interviews, examine the scene and ferry, review documents and gather evidence.
"We will then decide what, if any, further action to take. The investigation is expected to take several months to complete."
The Transport Accident Investigation Commission and KiwiRail were also investigating the incident, which KiwiRail earlier said had been caused by a steering failure.
No-one was injured in the grounding and there was no environmental damage.
KiwiRail chief executive Peter Reidy said Aratere would not operate again until it had been released by Maritime NZ.
At this stage, he could not give a timeframe for the ship's return to service, he said.
"We are working with urgency to understand what has happened here.
"This is an incredibly unfortunate incident, especially coming after an intensive investment in an enhanced maintenance regime, supported by global asset management peer reviews during 2023 and 2024.
"Since then, we've had a solid run with reliability and on time performance and have generally been pleased with how our ships are performing."
Aratere is New Zealand's only rail ferry, meaning it can be used to transport trains across the Cook Strait.
Its grounding has severed the rail link between the North and South islands. It is not yet known what impacts this will have on freight.