The Save Halkett Bay Marine Park Society filed court documents this week seeking an injunction to stop the plan to sink the 1960s former helicopter-carrying destroyer.
A spokesman for the group said it had a paint sample from the ship tested by an independent laboratory, which found highly toxic compounds called tributyltins.
These compounds are specifically designed to prevent the growth of marine life and it is illegal to dispose of them in the ocean, said Gary MacDonald.
"We don't understand why the government isn't forcing the proponents to prove the ship is clean instead of being dragged into court to make it uphold the law," he said in a statement.
The Artificial Reef Society of British Columbia announced Monday that it would sink the former HMCS Annapolis on Jan. 17, after being granted a permit by Environment Canada in October.
The ship is set to be towed to Halkett Bay off Gambier Island, just a short boat ride from Vancouver, and sunk in order to be used as an artificial reef and site for divers.
MacDonald's group has called for a third-party review of the permit issued by Environment Canada. The group alleges that inspectors did not properly test whether toxic polychlorinated biphenyls, also known as PCBs, that were earlier found in the ship had been cleaned up.
The Artificial Reef Society of British Columbia and Environment Canada did not immediately respond to requests for comment.
The society purchased the 110-metre ship from the federal government in 2008 with the intent of making it the largest artificial reef in the Greater Vancouver area.
It said the Squamish Nation and the Tsleil-Waututh Nation support the use of Annapolis as an artificial reef, and that it will help restore and preserve species like rockfish and ling cod.