Commerce Ministry spokesman Yao Jian told reporters that devastated regions of northeastern Japan contain clusters of manufacturers of electronics, cars, petrochemicals -- all key export items to China.
"Therefore, there will be an impact on bilateral trade in the short term," he said.
But he added it would "be limited" because "the Japanese economy will bounce back quickly."
Trade between the two nations totalled around $300 billion last year, or 10 percent of China's total foreign trade, Yao said.
Japan, which lost its 42-year ranking as the world's second-biggest economy to China in 2010, exports more products to the Chinese market than any other country, he said.
He said Japan also is the number five destination for Chinese exports.
The March 11 twin quake and tsunami disaster, Japan's worst crisis since World War II, has left nearly 22,000 dead or missing and entire communities along the northeastern coast destroyed.
Yao said major Chinese shipments to Japan, such as clothing, farm produce and electronic products, would also be impacted.