The survey was completed yesterday morning.
The 36-year-old vessel sank around midnight on August 5, 86km northeast of the Tonga's capital of Nuku'alofa, leaving 73 people, including a number of women and children, missing.
Yesterday Tongan police commander Chris Kelley said that police had revised down the number of people on the ship.
"We can confidently say that the number of persons reported on board the vessel now stands at 129," he said. Of that number, 54 men were rescued, two bodies were recovered and 73 people were still missing.
Other investigators from a six-person New Zealand Transport Accident Investigation Commission (TAIC) team have been reviewing information already gathered by the Tonga Police, which is running a separate investigation, confirming and interviewing witnesses and gathering additional documents to support the investigation into the ferry's sinking.
New Zealand's Associate Transport Minister, Nathan Guy, said yesterday the TAIC was formally supporting the Tongan Royal Commission's inquiry into the sinking.
"TAIC has had a six person team, including two investigators from the Australian Transport Safety Bureau and one from Maritime NZ, in Tonga since Wednesday last week working in the background pending the formal establishment of the Royal Commission."
Justice Warwick Andrew was sworn in as the Royal Commission's chair on Friday with two other commissioners yet to be appointed.
The TAIC team has been working closely with Justice Andrew since his appointment.
Mr Guy said the team would be conducting a wide-ranging and thorough investigation for the Royal Commission which would go well beyond the fateful voyage itself.
"The aim is that the Royal Commission's final report will establish the facts of the sinking, all the reasons contributing to it, and make findings and recommendations that will help improve maritime safety in Tonga and elsewhere."
He said TAIC's legislative mandate only allowed it to determine the circumstances and causes of transport accidents to avoid reoccurrences and it would not be involved in apportioning blame or liability for the tragedy.
The current team includes two master mariners, an engineer, a regulatory expert, a human factors expert, and a liaison and logistics person.
Mr Guy said it was envisaged the team would be in Tonga for another 10 days initially, with members returning as required to carry out inquiries and to support the Royal Commission. Other resources would be brought in if needed for specialist expertise depending on the course of the investigation.
The Manawanui was expected to return to Nuku'alofa after its successful mini-submarine mission to formally identify the sunken vessel.
Police intend to release pictures taken by the submarine tomorrow, after analysing the data collected.
