It is believed the association sanctioned a deal with fishermen who were asked to capture some of the dolphins for one of Waza members.
According to a report by the Guardian, in 2009 Waza allegedly agreed a "dolphin management protocol" with one of its members, the Japanese Association of Zoos and Aquariums (Jaza).
The agreement allegedly allowed fishermen to gather small numbers of dolphins towards shore for them to be captured for aquariums owned by Jaza. Excess animals would be then purchased by three other organisations, Dolphin Resort, Dolphin Base and the Taiji Town Development Public Corporation.
According to activists, the conditions of the aquariums where the dolphins are taken are appalling.
Sarah Lucas, the head of Australia for Dolphins, which has filed court action against Waza, said the association should enforce its code of ethics that bans dolphin hunts.
"For Waza to present itself as an animal welfare and conservation organisation and on the other hand support a member involved in one of the cruellest practices in the world, to the extent of helping them get preferential purchasing positions, is deceptive and harmful to the efforts to put the hunts to an end," Lucas said.
"Most zoos and aquariums around the world have no idea how Waza conducts itself behind closed doors. They will be very surprised to learn this."
The hunting season, which takes place annually, has often sparked protests worldwide with dozens of people protesting against the killing of hundreds of dolphins. Activists have also argued the season is not part of Japan's culture, contrary to what some believe.
The issue of dolphin hunting in Japan sparked international outrage after the release of the 2009 documentary The Cove, directed by former National Geographic photographer Louie Psihoyos, which shows the capture and slaughter of some dolphins during the hunting season.
The documentary claims more than 20,000 dolphins and porpoises are killed every year in Japan.