The launch, which sustained only minor damage, was escorted to Ōpua boatyard and placed under police guard until Maritime NZ staff arrived to take possession of it about 4pm.
A police spokesperson said officers and Coastguard volunteers cleared the ferry to ensure no one remained on board before the vessel sank about 2pm.
Police were continuing to assist Maritime NZ with the investigation and wanted to hear from all witnesses to the incident, or anyone who noticed a vessel being driven erratically earlier in the day.
They were urged to call the non-emergency police number 105 or Crime Stoppers on 0800 555 111, quoting file number 230413/1475.
As of Friday morning the skipper was still in critical condition in Auckland’s Middlemore Hospital.
Meanwhile, TAIC is conducting its own investigation and is also calling for witnesses and photos or videos of the two vessels.
Chief accident investigator Naveen Kozhuppakalam said he was also keen to receive any CCTV footage from businesses or homes with cameras trained on that part of the Bay of Islands.
“Getting the facts straight is vital, so we’re keen to hear as soon as possible from people who were on either vessel, anyone who saw the accident or the boats at any time in their journeys prior to the accident.”
Anyone who could help was urged to contact TAIC by emailing info@taic.org.nz.
A three-strong investigation team had arrived in the Bay to start collecting evidence.
The initial focus would be on gathering evidence that could disappear or change – not just flotsam from the impact, but also memories while they were fresh in people’s minds, Kozhuppakalam said.
Over the next few days, TAIC investigators would seek and recover any wreckage, secure electronic records – including photos, videos, and location data on people’s cellphones – and interview witnesses.
They would also gather information about the two vessels, including their individual and type histories, performance, maintenance, equipment and design.
TAIC had placed protection orders on both vessels and any objects that may have floated away.
Anyone who finds an item from the collision is allowed to pick it up to safeguard it, but must inform police or TAIC as soon as possible.
Each investigation has a different aim.
The police inquiry will determine whether anyone is criminally liable for the collision and injuries to the skipper.
TAIC only investigates incidents it believes could have significant implications for transport safety. It aims to make findings or recommendations to prevent such incidents happening again.
TAIC has in the past raised concerns about the lack of licence requirements for people operating recreational boats.