The Ministry of Trade, Industry and Energy said the WTO's Dispute Settlement Body made the decision in accordance with pre-established rules on handling trade disagreements, reports YonhapNewsAgency.
South Korea had rejected calls by Japan for a special panel on August 31, which the WTO respected, but the global trade body later accepted the second request made by the island nation earlier on Monday
The standoff comes after Japan claimed South Korea's ban on fish imports from eight prefectures near Fukushima violates established trade rules.
The ban has been in effect since September 2011 when it was announced that the Fukushima nuclear power plant, which was crippled by a massive earthquake and tsunami, dumped large quantities of radioactive materials into the ocean. Tokyo has periodically released nuclear waste into the Pacific as it tries to clean up the mess caused by the disaster.
South Korea has argued that the release of nuclear materials can contaminate fishery resources in the region and pose health risks. Importing fish from Japan can also hurt local fish consumption, because people cannot be certain where the fish they are buying originated. This can have a negative impact on local fishermen and the fishing industry as a whole.
The Fukushima accident is regarded as the worst nuclear incident in history along with the Chernobyl nuclear plant catastrophe in 1986.
The trade ministry, meanwhile, said once the panel is set up by the WTO secretariat, three experts will be picked to review the claims made by all sides and check all the legal aspects of the dispute.
Under WTO rules, the panel will have a year to make its report, although the final verdict can be delayed.
"The government in the future will actively justify the actions it has taken to protect the health of its citizens and point out the safety problems facing Japanese food and the way the country is trying to clean up the nuclear disaster," the ministry said.