The Oregonian reported that the complaint filed last week accuses the crew of the Shonan Maru No. 2 of ramming the Sea Shepherd's high-speed vessel Ady Gil, slicing it in half. Minor injuries were reported aboard the Ady Gil.
The suit says the Shonan Maru No. 2 is owned by Kyodo Senpaku Kaisha Ltd.
The lawsuit names as defendants Kyodo Senpaku and the Institute of Cetacean Research, a Japanese research foundation that oversees the whaling fleet. The suit seeks $3 million in damages.
A Portland law firm listed as representing the defendants didn't immediately return an Associated Press call for comment Monday.
In December 2011, the research institute and Kyodo Senpaku filed a federal lawsuit against Sea Shepherd in Washington state, alleging the conservation group interfered with the institute's "scientific research whaling." Last March, Sea Shepherd filed a counterclaim for the destruction of the Ady Gil.
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