The body, thought to be that of diving instructor Shoko Takahashi, was found at the weekend on Sempu island, East Java province, some 400 kilometres from where the divers went missing.
Five of the other female Japanese divers in the group were rescued days after they went missing on February 14 while the body of a sixth washed up on the Indonesian resort island.
The body found at the weekend was barely recognisable - the head was missing - but Takahashi's Balinese husband believes it is her due to the clothes inside the diving suit, police said.
"The husband, who came to the hospital last night, said he is 98 per cent sure that the body belongs to his missing Japanese wife."
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The body was flown to a hospital in Bali late yesterday, he said.
Takahashi was based on the resort island and with her Balinese husband ran the operator Yellow Scuba that took the divers out on the ill-fated expedition.
The captain of the boat that took them out has been arrested and faces a charge of "negligence which caused the loss of life" after leaving the divers alone in the open seas during the trip.
The survivors have told how the weather suddenly turned stormy and huge waves pushed them for miles before they managed to clamber onto a rocky outcrop near neighbouring Nusa Penida island.
They were eventually spotted on the outcrop and plucked to safety. They suffered dehydration and sunburn but no life-threatening injuries.