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The 24m Australian-flagged fishing vessel, Leila Jo, and Liberian-registered 180m bulk carrier, Rose Harmony, collided about midnight on January 12 off the coast of Lyttelton.
The fishing boat was damaged but made it back to Lyttelton unaided.
The Rose Harmony sailed to Dunedin.
Chief accident investigator Aaron Holman said there were clear rules around collision avoidance, and how those were applied would form part of the investigation.
"It's our understanding that the bulk carrier - the Rose Harmony, was departing Lyttelton for Dunedin and Leila Jo - the fishing trawler, was returning to Lyttelton where it was based."
"Our purpose is to determine the circumstances and the causes of accidents and incidents, with a view to avoiding them in future."
He said TAIC would be speaking to witnesses and assessing the vessels as part of the investigation as it worked towards making a recommendation, likely within a year.
An international vessel registration site showed the Leila Jo was built in 2000 by Adelaide Ship Construction International.
The Rose Harmony cargo ship was built in 2018 as a bulk carrier.
TAIC said initial reports indicated there were no injuries on either vessel, but that could change subject to its investigation.