China became the first foreign buyer of the system from Russia under a contract signed in 2014.
The vessel has brought back the damaged components to Russia's port of Ust-Luga for evaluation, Mariya Vorobyova, spokeswoman for the military and technical cooperation service told RIA.
They would be delivered to China at a later date, she said.
Russia also signed a deal to supply the S-400 missile system to Turkey late last year.
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