The boat grounded and capsized off Waimairi Beach late on Saturday night and was removed on Monday night. It was deemed unsalvageable.
Environment Canterbury regional harbourmaster Gary Manch said a marine salvage and rescue team removed the boat.
A Maritime New Zealand spokesman said an investigation into the incident has started and will involve interviewing people, a scene inspection and reviewing documents.
"All of that information will then be drawn together and a decision will be made on what, if any, further action will need to be taken," the spokesman said.
Three people were airlifted to hospital early on Sunday morning after the boat got into trouble off the coast. Police received a distress call at 11.09pm on Saturday.
A spokesperson said an officer located the struggling boat about 2km offshore about 11.35pm.
The boaties were rescued 30 minutes later.
Police say the boat was travelling from Akaroa to Kaikōura when it began spinning around in circles and then started taking in water.
All three boaties were taken to Christchurch Hospital.
The spokesperson said there was some fuel and debris on the beach, which posed a risk to swimmers.
Two people from the boat remain in a serious condition in hospital.
