New Zealand Defence Force figures show more than half a million litres of diesel fuel aboard the Manawanui when it sank has not been taken off it.

The survey ship sank off Samoa last October.

This week, Defence said it had finished the job of getting the fuel off, removing 365,000 litres, but Defence today told RNZ the Manawanui had 900,000 litres of diesel fuel on board - 535,000 more than taken off.

Defence said it did not know how much leaked, as some burned in a fire on board, before the boat sank.

"Some diesel fuel escaped through damaged tanks and pipes," Group Captain Rob Shearer said. "Our navy divers also worked hard to contain and capture ongoing leaks,"

Samoan authorities earlier estimated 200,000 litres leaked into the ocean.

Tests by the Scientific Research Organisation of Samoa showed the seawater and marine life were clear and uncontaminated, Shearer said.

The light diesel fuel dissipated relatively rapidly and evaporated, he added, citing "continuous environmental monitoring".

The sinking and leaking fuel closed fishing grounds important to local villagers for some weeks.

The fuel salvage was expected to last 20 days, but took almost three months.