The tremor hit Zigui County of Yichang City in Hubei Province at 3:42 am and its epicentre was located at five km below ground, according to the China Earthquake Networks Center.
No casualties were reported though the earthquake was felt across Zigui, state-run Xinhua news agency said.
"The minor earthquake has not affected the Three Gorges Dam, which can endure far stronger earthquakes," Hu Xing'e, vice head of the management bureau of the project with the China Three Gorges Corporation said.
She said that no earthquake-triggered landslides have been reported in the reservoir area and all power generating units and ship locks are working normally.
The dam, the world's largest water control and hydropower project which spans the Yangtze River, China's longest waterway, was unaffected by the 8.0-magnitude earthquake that hit the country's southwestern Sichuan Province in 2008.
On Tuesday, the water level of the hydropower project reached its designed full capacity of 175 metres in a storage test that allow experts to observe, research and validate the dam's original design and to test its hydropower turbo-generators.
The test marked the third round of the full-capacity storage test conducted since 2010.
"Wednesday's earthquake was a shallow-focus earthquake rather than a structural one," said Zhang Shuguang, head of the project's management bureau.
"It was not very destructive".
Zhang said the earthquake could have been triggered by water pouring into caves or the excavation of coal mine shafts in the region.
Since the dam started to hold water in 2003, about 19,000 earthquakes, most of which have been slight or ultra-slight, have been reported in the reservoir region, according Niu Xinqiang, head of the Yangtze River Institute of Survey, Planning and Design.
"No structural earthquake has been reported," he said.
Niu said that with the progress of the water storage tests, the banks of the reservoir are adapting well and becoming more stabilised.
"The frequency of earthquakes and landslides in this region has been lessening over the past years," he said.
However, critics of the dam allege that most of the tremors were caused by the weight of the mammoth water storage.