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The pictures clearly show the vessel's name plate, scattered debris and tangles of cables on the ship's deck.
The ship was intact and sitting upright, though one side is obstructed and the the submarine couldn't see the passenger deck.
The remotely-operated submarine was, however, able to take pictures inside the ship's cargo hold.
"The water clarity is reported to be very good and this has allowed the team to be able to conduct a good, thorough search of the sunken vessel," New Zealand Navy Lieutenant Commander Barbara Fleissner said.
The 36-year-old vessel sank around midnight on August 5, 86km northeast of the island's capital of Nuku'alofa.
Tongan police yesterday confirmed two dead, 73 unaccounted for and 54 survivors.
Of those unaccounted for, 67 were on the ferry when it sank, Tongan police commander Chris Kelley said.
The navy submarine had also photographed an upturned ambulance, believed to be that donated to the hospital on the outlying island of Hunga by a church from Bakersfield, California.
The vehicle was filled with medical supplies the congregation of the First United Methodist Church had been collecting for two years, news website Turnto23.com reported.
Meanwhile, the board of the Shipping Corporation of Polynesia Ltd (SCP), the Tongan state-owned organisation operating the vessel, have made their first public statement since the sinking.
Addressing a press conference on Monday, SCP chairwoman 'Alisi Taumoepeau extended the company's condolences and sympathy to families of those killed in the sinking, Tongan news website Matangitonga.to reported.
However, she said the company could not comment on the vessel's seaworthiness or how the sinking happened until the Royal Commission of Inquiry had been completed.
Families of those killed in the sinking had been camping outside SCP's offices since August 5, and the company was providing food, grief counselling and daily updates to them, she said.
"We also have a church minister to talk and pray with families and I think that is the most we can do at this stage," she said.
"We have a very small nation of 100,000 people and about 100 people are lost at sea, which just about touches everybody in the country. And we are just taking it one day at a time and we ensure that our support is ongoing for as long it is needed and just walk with the people."
