While the ship was in port, activists from Greenpeace attacked it and an accompanying vessel, the Kyo Maru. As Greenpeace personnel in Zodiacs harassed the crew, others attached themselves to mooring lines, anchor chains, and the bow of the ships. A chain was entangled in the propeller of the Kyo Maru as well. 

Eugene Lapointe, President of IWMC--World Conservation Trust, quickly reacted to the incident. "Vandalism is always a cowardly act," Lapointe stated, "and has no place in legitimate disagreement on issues." 

Japanese sources say the entire staff of the Nisshin Maru was entirely exhausted following the efforts to extinguish the fire and with the death of one of the crew members. 

Lapointe said that to attack a vessel in port following such a terrible incident is the height of cruelty and bad taste, and called for international censorship. While it was reported that Greenpeace had sent a letter of apology to the owner of the Nisshin Maru, Lapointe said this is in no way sufficient to clear the incident. "Greenpeace has proven themselves by this callous act, to be outside of the realm of rational consideration of issues and, as such, should be banned from participation in legitimate forums such as meetings of the U.S. National Oceanic and Atmospheric Agency, the International Whaling Commission, and CITES..."�