Union Minister of Shipping Sarbananda Sonowal posted on X saying "three Indian seafarers initially reported missing are now confirmed dead after bodies have been located and identified."
India's Foreign Ministry summoned a top US diplomat to lodge "a strong protest."
Earlier, India on Wednesday said it "condemned the attack on the commercial vessel Settebello off the coast of Oman," after the US military announced it had fired on a tanker attempting to breach its blockade of Iran.
It confirmed that 24 Indian crew members were onboard.
The US Central Command said American forces warned the crew before firing on the ship, which allegedly attempted to breach the naval blockade with a shipment of Iranian oil.