The flagship for the environmental group Sea Shepherd was expected to set sail from Shetland on Wednesday morning after it paid £520,000 into court to secure its release.

The Steve Irwin had been detained in Shetland more than two weeks ago after a Maltese company, Fish and Fish, raised an action for damages against the Sea Shepherd Conservation Society in a dispute over its direct action against the firm's bluefin tuna fishery last year.

The SSCS was ordered to deposit a bond of £520,000 by the court of session in Edinburgh on Tuesday, less than the sum originally sought by the firm: it is suing Sea Shepherd for $1.2m (£736,000) in damages and had sought £660,000 in security for the vessel.

There were significant fears that the ship, originally a Scottish government fishery protection vessel, may have had to be sold because the group would be unable to raise the money required.

The Steve Irwin, named after the Australian conservationist killed by a stingray in 2006, had been in Lerwick, the Shetland capital, before taking part in demonstrations against the Faroe Islands' annual pilot whale cull. The 40 campaigners on board the vessel hope to resume that action by joining its sister ship, the Brigitte Bardot, in Faroese waters this week.

Speaking from Sydney, Australia, Paul Watson, the group's founder, said he was confident the group would get their bond returned. He hopes to fly to Shetland on Friday to board the ship by helicopter.

"The bond has been paid, so the ship will seek port clearance in the morning and sail for the Faroe Islands," he said.

He added that he was encouraged by the response the protesters had received from Faroese islanders.

"The Faroese have not been killing any whales while the Brigitte Bardot has been there. We are making quite a bit of progress by talking to people. I find there is quite a lot of support for our position in the Faroes," he said.

"We find it encouraging that quite a lot of people in the Faroe Islands are not happy with the killing of the pilot whales."

Fish and Fish lodged its court action after Sea Shepherd released about 800 bluefin tuna from nets off Libya in 2010 because, the conservation group said, the Maltese firm was illegally fishing. The firm accused Sea Shepherd activists of injuring two crew after violent confrontations.

In a statement released last month, soon after the Steve Irwin was impounded, Watson said: "Fish and Fish are claiming damages for the bluefin tuna we rescued from their nets in June 2010, fish that we believe were illegally caught after the season had closed, without an inspector onboard, or any paperwork documenting the legality of their catch."