Sea Shepherd's founder and president Paul Watson has been arrested in Germany for extradition to Costa Rica.
The German police said that the warrant for Captain Watson's arrest was in response to an alleged violation of ships traffic in Costa Rica, during the filming of Sharkwater in 2002.
In a statement, Sea Shepherd said the incident took place on the high seas in Guatemalan waters, when Sea Shepherd encountered an illegal shark finning operation, run by a Costa Rican ship called the Varadero.
On order of the Guatemalan authorities, Sea Shepherd instructed the crew of the Varadero to cease their illegal activities and head back to port to be prosecuted.
While escorting the Varadero back, a Guatemalan gunboat was dispatched to intercept the Sea Shepherd crew.
The crew of the Varadero accused Sea Shepherd of trying to kill them, but video evidence proved this to be a fallacy, the organisation said.
It said that to avoid the Guatemalan gunboat, Sea Shepherd set sail for Costa Rica, where they uncovered even more illegal shark finning activities in the form of thousands of dried shark fins on the roofs of industrial buildings.
Sea Shepherd said conservationists around the world maintained hope that the Costa Ricans will drop the charges against Captain Watson, if they have not already been dropped.
"With Costa Rica's rich biodiversity, it would be a travesty for them not to stand up for sharks, which sit at the highest levels of the food chain assuring balance among ecological communities in the ocean."
While in jail, Captain Watson is being assisted by the European Parliament vice-president Daniel Cohn Bendit and the European deputy Jose Bove.
"Our hope is that these two honorable gentlemen can set Captain Watson free before this nonsense goes any further. The European Sea Shepherds have also mobilised to support Captain Watson."
As the plight of the shark becomes more desperate, Sea Shepherd Conservation Society has begun to outline a new shark campaign for 2012.
Julie Andersen, founder of Shark Savers and Shark Angels, joined Sea Shepherd to lead the organisation's global campaign to save sharks from extinction.
Sea Shepherd said it will use its expertise and experience to empower people around the world to take back their sharks – an animal critical to their, as well as the global, environment and economy.
The first stop will be the South Pacific, where the team will be headed in June.
"We've got all the laws we need to protect sharks. Now we will leverage our resources and expertise to help countries around the globe enforce them. Using Galapagos as a model, we will travel wherever we are needed - enforcing local laws while developing strategies and training locals to defend their sharks, fuelling world-wide enforcement efforts," Ms Anderson said.