Speaking to BBC Radio Wales Breakfast, Mr Green said there had “obviously” been a “large drop in animals using the area around Bardsey Island over the last 20 years”.
He said the decline in porpoises had been recorded elsewhere around the Irish Sea, but that “the amount of decline is variable”.
Mr Green added that climate change could be a factor, with fish population moving, leading to porpoise following them to catch food, while “they could just be feeding elsewhere”.
He also said there is not a huge fishing industry around the Welsh coast.
“But that could be an issue out in the wider Irish Sea and in international waters where large trawlers can operate and we know they do catch porpoises by accident,” he said.
“Whether they catch enough to decrease the population we don’t know, and that’s something that needs looking into.”
He added that the organisation was recruiting volunteers and training people to conduct sightings.
He also described the difference between a dolphin and porpoise, with the former being mainly bottlenose dolphins regularly seen in Cardigan Bay and near New Quay.
Porpoises are “a small animal with a very triangular, small fin on their back and you tend to only see them briefly as they come swimming up”.