The warning, in a joint letter to India's shipping regulator, was signed by the heads of six other representative bodies of shipping companies and ship owners.
It followed a protest march in Mumbai involving about 200 sailors against a spate of armed hijackings involving Indian crews.
More than 500 Indian sailors on over 20 ships are currently being held.
Seven crew members on a bitumen-asphalt tanker, the MT Asphalt venture, are still captive even though a ransom has been paid.
The unions called on the Indian government to step up its efforts to combat piracy by lobbying at the United Nations.
Somali transitional government's Foreign Minister Mohammed Abdulahi Omar Asharq told a counter-piracy conference in Dubai last week that the world is losing the battle against the pirates.
The international policy of "containment" through naval patrols off the Somali coast is not working, he said.