Work is underway to figure out how to recover a shunt train and its wagon carrying empty tank containers from Picton Harbour.
It plunged off the wharf on Wednesday afternoon at the berth usually used by Interislander ferry Aratere.
The ferry was in Wellington at the time and remains there.
The incident occurred while the remote-controlled shunt and wagon were being manouvred in the rail yard. No-one was injured.
The wagon is partially afloat and was secured to the wharf overnight while the locomotive, weighing about 50 tonnes, is believed to be lying in about eight metres of water.
"We anticipate sending divers down to determine the position of the loco, which may need to be floated to a different area to lift it out of the water," KiwiRail Chief Operating Officer Todd Moyle said, who is overseeing the recovery effort.
He said there is no sign in the water that the locomotive’s diesel tank has ruptured, and the sea conditions are calm.
"Nevertheless, this will be a complex recovery and our priority is the safety of the people involved, and the protection of the marine environment.
"KiwiRail is grateful to Port Marlborough for their support and assistance and apologises for the disruption to the port."
Bluebridge and the Interislander ferry Kaitaki are continuing to operate from berths in Picton.
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