The ship was intercepted Saturday off the western state of Gujarat, the coast guard said in a statement.
"This is the largest single haul of narcotics seized till date," it said, adding the drugs were worth an estimated $545 million.
An undisclosed number of suspects were detained for questioning by coast guard officials, police and intelligence agencies.
Anyone caught smuggling or possessing narcotics is remanded in custody without bail under Indian law.
Last year police in the western state of Maharashtra seized 18.5 tonnes of ephedrine, a precursor used in the manufacture of methamphetamine, worth $311 million.
In 2013 police in the holiday resort state of Goa arrested a 45-year-old Briton in possession of more than four kilograms of amphetamines worth $330,000.
Heroin seizures in India have increased in recent years, figures from the Narcotics Control Bureau show.
Heroin, largely from Afghanistan and smuggled through neighbouring Pakistan, makes its way into India through the disputed northern state of Kashmir and coastal border areas in the west.
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