Deputy Foreign Minister Li Hui also told Russian Ambassador Sergey Razov that China "cannot accept the incident and expresses strong dissatisfaction," according to a statement posted on the Foreign Ministry's Web site.
Li called on Russia to do its best to search for eight crew members who went missing after the sinking in waters near Vladivostok.
"China was shocked by this incident," he said.
Russian news agencies reported earlier that Russian border guards opened fire last weekend on the Chinese cargo ship as it sailed off the Russian far eastern port city, and that it later sank in a storm.
Russia's Interfax news agency said the New Star, carrying a crew of 16 sailors from China and Indonesia, was fleeing border guards in the Sea of Japan when the shooting occurred. The guards were pursuing the ship because it had left the port of Nakhodka without notifying authorities, it said.
On Friday, Interfax quoted Russia's Foreign Ministry as saying that the captain of the ship was to blame because he violated border laws and refused to stop his ship when warning shots were fired.
"We regret the tragic consequences of these events. However, we lay the whole responsibility for what happened on the New Star captain, who acted extremely irresponsibly," Interfax quoted ministry spokesman Andrei Nesterenko as saying.
Interfax earlier said the New Star had turned around after being shot at but started sinking as a storm struck.
The sailors jumped into two lifeboats but strong waves overturned one of them and border guards were only able to rescue eight crew members, it said.
Chinese Foreign Ministry spokeswoman Jiang Yu said Thursday that 10 members of the crew were Chinese and only three had been rescued.
Interfax said rescuers had searched the freezing waters for the bodies of the missing sailors.
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