Some of the paintings have been damaged by mud and silt while others have peeled off or cracked due to the rain.
The paintings in Ningxia Hui Autonomous Region carved on individual rocks were more seriously damaged as floods washed the rocks away.
An employee with the scenic area, which has about 6,000 cliff paintings, told state-run Xinhua news agency that about a dozen paintings on individual rocks remained unaccounted for.
The unusually heavy rain resulted in rare floods in the mountain.
Most defenses were destroyed by the powerful water flows, resulting in the devastating damage to the cliff paintings, said Hu Zhiping, deputy director of Helan Mountain Cliff Painting Administration in Yinchuan City, capital of the region.
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Helan Mountain has around 20,000 cliff paintings carved by the nomads that once lived in northern China.
The paintings are scattered over several hundred kilometers. The paintings depict herding, hunting, sacrificial rites and life episodes of the people who lived 3,000 to 10,000 years ago.
Images of animals dominate the paintings, followed by figures, vehicles, plants, planets, fingerprints, written characters and abstract signs.