"They have assaulted and kidnapped two of my crew," Paul Watson of the Sea Shepherd's Steve Irwin told Fairfax Media as his ship chased the whaler with his men aboard.
Japan's Institute for Cetacean Research confirmed two anti-whaling activists were being held, but institute director-general Minoru Morimoto has denied the men were tied up.
By around 11pm Australian Benjamin Potts and Briton Giles Lane had been held for five hours on the harpoon ship Yushin Maru No 2.
Earlier in the day they had gone aboard the whaler to deliver a letter, saying they had done so because the Japanese had refused to acknowledge radio communications.
"I am not boarding your ship with the intent to commit a crime, to rob you or to inflict injury upon your crew and yourself or damage to your ship," the letter said.
The were delivering the message and then "request that you allow me to disembark from your vessel without harm or seizure."
Mr Morimoto confirmed the two men had been taken into custody, and said they were taken to a secure room.
"Any accusations that we have tied them up or assaulted them are completely untrue," Mr Morimoto said.
"It is illegal to board another country's vessels on the high seas. As a result, at this stage, they are being held in custody while decisions are made on their future," he said in a statement.
"The two boarded the Yushin Maru No 2 after they made attempts to entangle the screw of the vessel using ropes and throwing bottles of acid on to the decks."
But Watson said as the two boarded Yushin Maru the Japanese attacked them.
"First of all they tried to throw Benjamin Potts overboard, but he managed to get his way out of that.
"Then they assaulted Giles Lane. He seems to be in some pain. They tied him up incredible number of ropes.
"It looks like some kind of bondage movie. Its ridiculous."
- With AAP
* Listen to Sea Shepherd skipper Paul Watson talk to Fairfax Media's Michael Field about the two protesters held by Japanese whalers.
- Fairfax Media