The incident took place last night around 10 PM on barge 'Orion-2', which was carrying grains, nearly 4 nautical miles off Malabar Hills shore.
According to police, the toxic gases generated inside the cavity due to stocked grains and water.
When the six sailors went up to the cavity for some cleaning work, they came into contact with the toxic gases and inhaled it, resulting in death of three of them, while others suffered suffocation, a personnel at Yellow gate police station said.
Soon, Coast Guard boat C-154 was rushed to the spot and initiated the rescue operation, he added.
The victims were first taken to India Dock and later shifted to Bombay Hospital for treatment, the official said.
The deceased were Mangesh Bhosle (27), K T San (27) and Jayanta Chaudhary (24). Those hospitalised were identified as Dhahur koriar, Sharmasan Mandal and Ganesh Bhahiya, police said.
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