Witness Cherie Curchod said she saw the whale thrashing around near a jetty below her home after it was given more than six injections.
Ms Curchod said the whale was then tied up and dragged across the bay at Bonnie Doon, to The Basin at Pittwater before it ``actively started trying to get away''.
"Then they dragged it to a closed tent and all the while they dragged it, it was flapping it's tail, blowing out of it's head and moving and trying to get away,'' she said.
"It was so upsetting because euthanasia is meant to be an easy death and that whale did not have an easy death at all.''
Divine Marine Group spokesman Alexander John Littingham said he was on his boat just outside a restricted zone, protesting against the euthanasia, when he witnessed it.
"It looked like a scene out of the Antarctic with a Japanese fishing boat. It was absolutely disgusting,'' Mr Littingham, a sea captain, told Fairfax Radio Network.
"They have towed him behind the boat, scenes reminiscent of what we've seen the Japanese fishing trawlers do, dragged him 400 metres across the bay.
"He was clearly still alive, he was clearly moving, the line was thrashing, then they've dragged him up onto the beach and put him into a tent and now we can't see what's happening and there's a possibility the whale was still alive when he arrived on the beach.
"We're complaining about what the Japanese are doing in the Antarctic and we're allowing it to happen in Pittwater.''
