The head of the Dunedin Tongan community, the Rev Sione Pule, said family had advised him an aunt, cousin and a 2-year-old niece were missing.
Mr Pule, who visited Tonga last month, said the Tongan community in Dunedin would raise money to support family and friends affected by the tragedy.
"It is terrible news."
Information was slowly coming from the island and "we are waiting to find out more".
Members of the Dunedin Tongan community had been contacted, and while initial reports indicated no immediate family were involved, more was expected to be known today, Mr Pule said.
Special services will be held at Tongan churches throughout New Zealand today and tomorrow.
About half of the 100-strong Tongan community in Dunedin had strong connections to the area near where the ferry - MV Princess Ashika, which was heading from Nuku'alofa to Ha'afeva, in the Nomuka Islands group - sank on Wednesday night.
Mike Roberts, of New Zealand's Rescue Co-ordination Centre, said last night of the suspected 86 people on board the ferry, 53 had been picked up safe and well and two bodies found.
However, reports of the number of people on board varied and it was possible more than 100 were on Princess Ashika when it sank.
"Tongan police are working to establish exactly who is still missing and [they are] liaising with next of kin," Mr Roberts said.
A Royal New Zealand Air Force Orion searched the area until dark last night and was scheduled to resume this morning.
Four vessels, including Tongan Navy vessel Pangai, also searched last night.
Foreign Affairs Minister Murray McCully said Prime Minister John Key had expressed New Zealand's sympathy to Tongan Prime Minister Dr Fred Sevele.
Both leaders were attending the Pacific Islands Forum in Cairns.
The Ministry of Foreign Affairs and Trade had had no calls from anyone about other New Zealanders, Mr McCully said.
New Zealand would help with marine safety issues, which would "definitely come under scrutiny".
Ha'afeva man Siaosi Lavaka told the Matangi Tonga website only the men had reached the lifeboats after the ferry was overturned by heavy seas.
"No women or children made it," Mr Lavaka was quoted as saying after being returned to shore with about 50 other male survivors.
Mr Lavaka, who was travelling with his mother, Lavinia, who remains missing, said waves went into the lower deck of the ferry where the crew were.
He woke to find the ferry rocking violently and waves breaking over the lower deck.
The rocking apparently moved cargo to one side of the vessel, unbalancing the ferry and turning it over, he said.
"We woke up to the sound of shouting and we jumped off," he said.
Seven of the nine lifeboats were filled with male survivors.
Another lifeboat was empty, and a ninth drifted away.
Mr Lavaka believed the women and children were sleeping and all were stuck inside the ferry when it went down.
Frances Oakes, of Oamaru, said she contacted family "first thing" in Nuku'alofa yesterday morning.
While no immediate family were involved, "I am sure some of my extended family will be".
"It is a terrible tragedy. More than 30 years ago I lost uncles and cousins when a ship sank, so it reminds me of that," she said.
Oamaru had a "growing" Tongan population, so "there will be people affected by this".
Mrs Oakes said the area where the Princess Ashika sank was not known as a dangerous area for vessels.
"It is very unusual."
RCCNZ launched the rescue response after the Maritime Operations Centre picked up a mayday call from just before 11pm on Wednesday.
It was not yet known what caused the sudden sinking of the ferry, which was carrying 10 tonnes of cargo.
