The ultimatum is part of a revised national action plan on the illegal ivory trade. Thailand will present the plan to the Convention on International Trade in Endangered Species of Wild Fauna and Flora (Cites) this month.
The plan has been drawn up after the Cites Standing Committee criticised Thailand's efforts to deal with the illegal ivory trade as "unsatisfactory" at its meeting in Switzerland in July. The panel also expressed concern over delays in changing laws to deal with the problem.
Thailand has banned trading in ivory from wild and African elephants, but not domesticated elephants. Environmentalists say this opens a "loophole" for the illegal trade, since telling apart ivory from various sources is difficult.
Deputy department chief Thanya Nethithamakul said the revised plan includes the requirement for ivory shops to register and declare their stocks.
Officials will review the revised action plan once more before submitting it to government for final approval.
"We will give ivory shops about two months to register. If they continue to ignore the order, we will take legal action against them. The registration will help us know where these shops are and how much ivory each of them possesses," he said.
He added the Council of State is considering two bills on the issue.
One seeks to imprison people found in possession of African ivory while the other would require people who possess ivory from domesticated elephants to declare the products with the authorities.
"I am confident that Cites will not impose a ban on fauna and floral trade in Thailand after it considers the plan," he said.
"But the most important thing is that we must implement each proposal within the promised timeframe."
The department will launch its campaign against the illegal ivory trade at Chatuchak weekend market, followed by inspections of ivory shops nationwide.