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.
On Saturday, the Myanmar government said it was not responsible for the migrant boat crisis and said it might not attend a summit on the issue being hosted by Thailand on 29 May.
As international concern over the migrants grew, Malaysian Foreign Minister Anifah Aman held talks with his Bangladeshi counterpart Abul Hassan Mahmood Ali on Sunday to try to find a solution to the crisis.
Rohingya Muslims have been fleeing Buddhist-majority Myanmar – also known as Burma – because they are not recognised as citizens and face persecution.
Many of the Bangladeshis at sea are thought to be economic migrants.
Early on Sunday there were reported to be at least five people-smuggling boats, carrying up to 1,000 migrants, moored just off the northern coast of Myanmar.
Because Thailand and Malaysia are stopping the boats landing, the smugglers are now reluctant to make the journey but are refusing to release those on board unless ransoms are paid, says the BBC’s Jonah Fisher in Myanmar’s main city, Yangon (Rangoon).