"To euthanize the animals all in one shot, all in the first day — it just makes no sense," said David Chan, who worked with the province to develop its prohibited species list.
Conservation officers said the owner of the pythons did not have permits and many of the animals were on the province's list of prohibited species.
They also called them a risk to public safety, but Chan disputes that claim.
"I'd like the Ministry of Environment to prove they have actual evidence these animals are what they call a public safety issue," said Chan.
Conservation officers also told CBC News on the weekend they had nowhere to house the snakes.
"We don't have the capacity to store 46 controlled alien species snakes, so we can't take any sort of risk, so we had to have those animals put down" said conservation officer Dave Cox.
Chan, the owner of Exotic Serpents in Richmond, B.C., questions that decision as well.
"They took no opportunity to try to relocate these animals."
Meanwhile, he says he's worried all the negative press snakes are getting will result in the public calling for further bans, which, Chan argues, will only push demand for exotic pets to the black market.