Survivors told of horrific conditions. Three men separately said people were stabbed, hanged or thrown overboard.
The 700 rescued migrants from Myanmar and Bangladesh are being processed by the Indonesian authorities.
Thousands of migrants are estimated to be adrift in South East Asian waters, denied permission to land.
The BBC’s Martin Patience, who spoke to some of the survivors in the Indonesian port of Langsa, cautions that their accounts cannot be verified.
However, three migrants made similar statements in separate conversations.
If true, the claims will add to the growing international pressure on Asian countries to find a solution to this crisis, our correspondent says.
The migrants had wanted to land in Malaysia but say they were driven away by the Malaysian navy.
The boat had reportedly been at sea for two months and had been recently deserted by its crew when it was rescued by Indonesian fishermen on Friday.
The survivors are now being sheltered in warehouses on the shore in Langsa. Many are suffering from malnutrition and dehydration.
The Myanmar government has insisted it is not responsible for the migrant boat crisis and said it might not attend a forthcoming summit on the issue.