Farmers held protests in South Korea recently when Seoul and Washington were discussing trade deals.
"Agriculture will be the most difficult for the two nations, and Chinese manufacturers may face challenges from imports of goods from Japan and South Korea if the FTA is signed," Jiang said.
"We will push the FTA gradually, working on the easy part before tackling the difficult part," Jiang said.
Wang said South Korea probably has little interest in the trilateral trade pact and is more focused on negotiations with China.
South Korea and Japan compete with each other in some industries, and that may make the trilateral talks difficult, Wang said
Concluding an FTA can be time-consuming. For example, China and Australia started discussions eight years ago, and talks are still ongoing.
In July 2004, China and the Gulf Cooperation Council launched FTA talks, but no trade pact has been agreed to yet.
China has already signed FTAs with 10 nations and regions, including ASEAN, Pakistan and New Zealand, according to the ministry, and China is in negotiations with other countries including Norway and Iceland.