Not-for-profit organisation Life Investigation Agency (LIA) has been documenting the hunt since September and filmed the moment the young whale, nicknamed "Hope", was killed yesterday.
Distressing video shows the whale being driven between two boats in "The Cove".
Fishermen tied a rope around the whale's tail before securing it to a boat. The whale was hauled upside down, and held underwater for 20 minutes.
LIA director Ren Yabuki witnessed the killing.
"It violently thrashed as blood splattered around, but the fishermen were laughing while working," he told 9news.com.au.
"I witnessed the agony and my hands were trembling."
The Taiji dolphin hunts run from September 1 to February 28. Nine species are permitted to be killed and caught.
Minke whales are not listed as one.
Mr Yabuki explained the rules around capturing minke whales are complicated as they're a species that falls under commercial whaling.
However, that does not make the killing at Taiji illegal, he explained.
"Killing minke whales can only be done by authorised persons and during the permitted period. However, in the case of a fixed net, it basically has to be released
"However, Japan has resumed commercial whaling and if minke whales enter the set net, they will be allowed to catch them by collecting DNA samples," he said.
'Sad' fight for survival
In the days before the whale's death, Mr Yabuki said the animal made repeated attempts to escape.
"He was trying to get out of the net by attacking the net over and over again, hitting his head and back against the net," he said.
"When Hope realised that wasn't the case, he began spinning in small circles...the same anomalous behavior as the animals in aquariums
"Hope was trying hard to live. It was very pitiful. I was very sad."
Advocacy groups had been calling for the whale's release for weeks, but Mr Yabuki believes fishermen wanted to kill the animal the moment it became trapped.
He claimed fishermen made one 10 minute attempt at release on December 24, 2020 — the day it was caught.
"During the 19 days they had a lot of chances to release," he said.
"The fisherman said, 'the current is so fast that you can't let it escape,' but there were many days when the current was gentle and when the sea was calm.
In a statement the Fisheries Agency of Japan (FAJ) Whaling Affairs Office said:
"If whales are incidentally trapped in set nets, as a principle, FAJ asks the fishermen to release them as far as it is safe and possible to do so.
"However, if it is considered impossible to do so, as an exception, they are allowed under the national legislation to use them for food or properly dispose of.
"Bycatch shall be taken into consideration when calculating the catch limits for whaling in line with the Revised Management Procedure (RMP), which is a strict and robust procedure developed by the International Whaling Commission (IWC)."