The Haixun-31 sailed on Wednesday and will monitor shipping and "protect maritime security" on its way to Singapore, state media said.
A Chinese foreign ministry spokesman described the trip as routine.
Several Asian nations claim territory in the waters that include shipping lanes and may contain oil and gas.
The Philippines and Vietnam recently accused Chinese vessels of aggressive actions in the South China Sea.
On Monday Vietnam staged a live-fire exercise in the area which Chinese state media denounced as a military show of force.
The 3,000-tonne Haixun-31, operated by the Chinese Maritime Safety Administration, will pass near the Paracel and Spratly island groups. officials said. The islands are at the heart of disputes with other governments.
The official Beijing Daily newspaper said the ship - which has a helicopter pad and can stay at sea for up to 40 days - would monitor shipping, carry out surveying, inspect oil wells and "protect maritime security".
Earlier this week, Beijing said it would not resort to the use of force to resolve its maritime border disputes.
Vietnam, China, the Philippines, Taiwan, Brunei and Malaysia have competing claims to the Spratlys while Beijing and Hanoi are in dispute over the Paracels.
Hanoi, which chaired the regional grouping Asean last year, has actively promoted a multilateral solution. However, China says it prefers to negotiate with individual states separately.
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