The dead whale brought into Tauranga's port on the bow of a ship on Wednesday has been buried.
The ship arrived at the Port of Tauranga about 11.30am with the whale slumped across the bow.
Department of Conservation spokeswoman Margaret Metcalfe said the whale was towed to a "secluded" spot on Tauranga Harbour yesterday afternoon and respectfully buried. The department would not be disclosing the exact burial spot, she said.
It was not clear exactly when on the ship's journey between Brisbane and Tauranga the whale was hit.
Before burial, genetic samples were taken to confirm the whale's species and sex.
The whale was initially reported to be a Bryde's whale but Ms Metcalfe said that was no longer thought to be the case.
The genetic samples would be sent to a lab at the University of Auckland.
Tauranga-based Department of Conservation ranger Karl McCarthy said it was thought to be a sub-adult male Sei whale. If that assessment was correct, it would be the second recorded incident of the species being struck by a boat in New Zealand waters, he said. The first was in Auckland in 2001.
A Sei whale also washed up dead on a Bay of Plenty beach in 2008.
"The Sei whale is a migrant species considered endangered globally. It can be found throughout New Zealand waters but is not common."
There were 15 confirmed sightings of Sei whales in New Zealand dating back to 2004. Mr McCarthy said the species was difficult to identify.
"It's likely that people see them but can't identify them so they get recorded as an unidentified baleen whale."
The whale was 12.7m long. Adult male Sei whales could grow in excess of 18m long.
The Bay of Plenty Times attempted to contact Tauranga Moana iwi representatives who worked with the department on what to do with the whale, but no one was available for comment.