The move came after the existing Youyi Guan checkpoint on the Vietnam border was overwhelmed with 15-kilometre-long queues of Thai and Vietnamese goods vehicles.
The department, together with National Bureau of Agricultural Commodity and Food Standards, had earlier raised the border-traffic problem with the General Administration of Customs of China (GACC).
China responded by opening the Dongxing and Pingxiang border gates in Guangxi for imports of Thai fruits from the Vietnamese side.
The former has capacity to serve over 2,000 trucks a day, while the latter allows the fruits to be transported by train.