The boat carrying 45 people - tourists from Kanchi Puram district of Tamil Nadu and Mumbai, and crew members -- sank on its way from Ross Island to North Bay.
The South Andaman district administration confirmed 21 deaths and said 13 people were rescued.
Civil administration and defence establishments like the Coast Guard conducted operations to rescue remaining passengers, the sources said.
It was suspected that some persons might have been trapped in the cabin of the boat 'Aqua Marine'.