The group alleges that Bethune broke Sea Shepherd policy by bringing a bow and arrows on to the Ady Gill, which later sunk after colliding with a Japanese ship in the Southern Ocean this year.
• Decision to ban Bethune was to help him, says wife
The decision to bring weapons aboard the ship broke the group's policy of "aggressive but nonviolent action", Sea Shepherd chief executive Chuck Swift, said in a media release.
"His decision to bring them on a Sea Shepherd campaign is unacceptable," he said.
"He will no longer be formally associated with, or be a representative of the Sea Shepherd Conservation Society."
The group would still support Bethune with his legal battle in Japan, Mr Swift said.
Bethune has admitted to four charges in relation to boarding the Japanese whaling fleet's security ship the Shonan Maru II.
He has pleaded not guilty to one charge of assault and faces up to 15 years in prison if convicted of all charges.
After three days of hearing in Tokyo District Court last month, closing arguments will be heard on Thursday. A verdict is expected this month.
