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.
She gave no details about the damaged components but described them as secondary.
Russia also signed a deal to supply the S-400 missile system to Turkey late last year.
(This story has not been edited by NDTV staff and is auto-generated from a syndicated feed.)