Andrew McMillan, a New Zealand navy commander, told public radio that the search was suspended on Monday because of "increasingly bad'' weather that was not expected to improve until Tuesday.
He said the water clarity was good but the seabed where the ferry went down was uneven with depths ranging from 100m to 800m in some places, making search conditions difficult
The search team's equipment was effective up to 115m.
|Search teams suspended the operation due to bad weather [Reuters]
"With the topography, with the uncertainty of where the vessel has gone down, we have to face the realisation that we might not even be able to find it," McMillan said.
On Saturday navy divers from Australia and New Zealand began looking for the wreck using an unmanned explorer submersible to search an area from where an emergency distress call was broadcast from the ferry - about 85km northeast of the capital.
So far nothing has been found, and the cause of the disaster is still unknown.
Survivors described the ferry rocking violently from side to side and waves breaking the lower deck before it went under, despite officials say that weather conditions were mild.
The ship went under in less than a minute, giving passengers below decks little chance of escape.
|The cause of the disaster is
still unknown [AFP]
Services across the archipelago were held on Sunday, as local residents offered prayers for the missing.
Similar services were held in New Zealand, where thousands of Tongans live.
"A great tragedy has swept this island nation - the Friendly Islands - our beloved islands," Salote Lilo, a Tongan church member told a 1,000-strong congregation in Auckland.
The confirmed dead were a British man living in New Zealand and a Polynesian woman.
One Japanese citizen, and two each from Germany and France were among the missing, police have said.
Ten children were unaccounted for along with at least 33 women.
Tonga, an archipelago of 169 islands and 120,000 people, is located about two-thirds of the way from Hawaii to New Zealand.
The island is regularly hit by cyclones and lies near an earthquake fault-line, but few natural disasters have caused many deaths.