The U.S. Coast Guard said the Massachusetts-based vessel, the ESS Pursuit, caught the canisters Sunday about 45 miles south of Long Island. The crew threw the canisters back into the ocean when the man began developing blisters.
The boat remains isolated off the coast of New Bedford.
The U.S. military used the ocean as a dumping ground for munitions, including a mustard agent, from after World War II through the 1960s.
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