Akemi Kato, 52, failed to show signs of life as an ambulance carried her to Krabi Hospital.
Phuketwan has been told that Mrs Kato had never snorkelled before.
She got into difficulties at Kai island, a short ride by traditional longtail boat from the resort town of Ao Nang, or Railey, where the family was staying.
Needless deaths have been occurring off Phuket especially because tourists are often not taught how to use a snorkel before going into the water with one.
Often, someone who is taking in water through a snorkel will show no obvious signs of being in distress.
Some time later, people nearby will notice they are not moving.
The death of a Japanese tourist is unusual.
Most previous snorkelling-related drownings have occurred among Chinese visitors, who are coming to Phuket and Krabi in increasing numbers.