Fisheries Administration vessels Yuzheng 311 and Yuzheng 202 left Sanya, Hainan, on Thursday, China News Service reported.
The semi-official news agency quoted a fisheries administration official as saying the ships would be working alongside the fishing fleet, offering protection and rescue assistance.
The patrol's departure follows protests by Vietnam this week after a mainland patrol ship seized a Vietnamese fishing boat and its 12-man crew on March 22.
A statement posted on the Vietnamese Foreign Ministry's website on Monday called for the "immediate and unconditional release" of both the crew and the vessel, which were captured in the Paracel Islands, another disputed group lying between the Spratlys and Hainan.
The vessels' departure also coincided with the end of a four-day visit to China by Vietnam's deputy foreign minister, Pham Binh Minh.
The Spratly Islands - known as Nansha in Chinese - are one of the region's hottest potential flash points.
Beijing, Taipei and Hanoi claim ownership of the chain, while some of the islands are also claimed by Brunei, the Philippines and Malaysia.
The rich fishing grounds are believed to contain extensive oil reserves. The islands are also of crucial strategic importance owing to their proximity to major shipping lanes.
Beijing claims sovereignty over the Spratlys based on archaeological evidence that Chinese fishermen have been trawling in the waters since 112 BC.
Fisheries officials say that since 1994 there have been more than 300 attacks on mainland fishing vessels in the region, resulting in the deaths of 25 fishermen.
The Yuzheng 311, a converted naval patrol boat, is the administration's largest and most advanced ship. It was first posted to the South China Sea in March last year.
Vietnam has been beefing up its maritime defences in response.
Hanoi cut an arms deal with Russia in December to buy six Kilo-class submarines - widely interpreted as a move to counter China's increased assertiveness in the South China Sea.
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It's unbelievable that China's claims to the Spratlys (as stated in the article) is based on the fact that there were Chinese fishing in the waters around there in ancient history. Jeez, if countries were able to claim territories on this kind of reasoning, all the countries in the world would be at war with each other.