The captain of the anti-whaling ship, the Steve Irwin, has been arrested in Portugal on an outstanding 30-year-old arrest warrant.

Paul Watson was arrested at Madiera airport as he arrived for this week's meeting of the International Whaling Commission (IWC) in Portugal.

The Australian director of the Sea Shepherd Conservation Society, Jeff Hansen, says Mr Watson was released after four hours of questioning.

"This warrant was actually issued back in 1980, which was in response to Sea Shepherd ramming and later scuttling the pirate whaler the Sierra," he said.

"Then Paul had lengthy discussions with the police in northern Portugal and they determined that the warrant had actually expired in 2008 so there was no valid reason for them to hold him."

Mr Watson says he was released after authorities discovered the warrant for his arrest had expired.

"A little surprised because I've come and gone in Portugal many times and so suddenly why this happened I don't know," he said.

"But it was like last year in Chile, I was hassled a bit... Chileans told me it was because Japan had put in a complaint and they wanted to question me about what I was doing at the International Whaling Commission meeting.

"So I'm not really quite sure if Japan was behind this."