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Police commander Chris Kelley said it was now believed there were 149 people on board the Princess Ashika, which went down just before midnight on Wednesday.
Two bodies and 54 survivors have been found, and 93 people are unaccounted for.
Police said the final number could be higher and they were continuing to analyse information about unrecorded people on board the vessel, whose official manifest showed only 79 passengers and crew.
"I think there is a complete manifest that is held by a crew member on the boat when it sailed, but of course that would have been lost in the sinking," Kelley said.
"What we are faced is that people are telling us is they put people on the boat and they weren't on the manifest that was supplied here."
Navy divers from Australia and New Zealand were to continue on Sunday trying to locate the ferry, which was en route from Tonga's capital Nuku'alofa to outlying Ha'afeva when it sank moments after issuing a mayday call.
Survivors said it went down quickly when cargo appeared to shift and people below decks had no time to escape.
The ferry was initially located in about 35 metres (115 feet) of water but may have slipped further on the uneven seabed to a depth of about 100 metres.
Kelley said he was unable to comment on the cause of the tragedy but police had interviewed the ferry master who confirmed survivor reports of how quickly the disaster unfolded.
A distress call was sent out at 11:50pm and only a few minutes later the emergency beacon went off, which happens when a ship is immersed in water.
In a small nation of 100,000 people, a large number of families would know people on board the ferry, Kelley said as mourners paid their last respects in churches across Tonga.
Survivors have described how they saw the ferry hit by a one-metre wave which swept the cargo to one side, causing the vessel to overturn.
"The ferry sunk so quickly that no one was able to do anything, and I think the passengers inside just couldn't make it out in time because the ferry just overturned and sank so quickly, in a minute," survivor Viliami Latu Mohenoa said.
Although questions have been raised about the seaworthiness of the Princess Ashika, Tonga's Prime Minister Feleti Sevele said it had passed safety inspections and was found to be suitable for insurance.
Tongan Transport Minster Paul Karalus said an inquiry into the tragedy would be conducted by a marine investigator from New Zealand.
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