The New Star sank shortly after turning back to port in heavy seas
China has called on Russia to carry out a full investigation after a shooting incident on Sunday involving a Chinese-owned vessel off the port of Nakhodka.
Eight sailors went missing after Russian border guards opened fire.
Russian says the freighter, which later sank, was being investigated for possible links to smuggling and had set sail from Nakhodka without permission.
It is still unclear what caused it to sink, although it is said to have tried to turn back to port in heavy seas.
On Wednesday, a Russian FSB border control department spokesman admitted one of its ships had fired more than 500 rounds at the fleeing New Star during what was initially presented as a rescue.
At a news conference in Beijing on Thursday, Chinese foreign ministry spokeswoman Jiang Yu said three Chinese crew members had been rescued after the incident and that seven others were still missing in the Sea of Japan.
The remaining six members of the New Star's crew were Indonesian, Russian officials said. One of them is reported to be missing.
Ms Jiang said China had called on Russia to "to spare no effort to help search for the missing crew members and quickly find out the causes of the incident".
She declined to comment further on the shooting, although said the freighter had "encountered danger".
The vessel's owner, Hong Kong-based J-Rui Lucky Shipping, condemned the Russian authorities and called for a joint investigation panel to be set up to find out who should be held responsible.
It said the New Star had arrived in Nakhodka at the end of last month to deliver a consignment of rice, but that the purchaser had refused to accept it, saying it was poor quality, and demanded compensation.
The company said officials in Nakhodka had dragged their feet giving the vessel clearance to leave, prompting the ship to depart without permission on Sunday.
The Russian border control department has blamed the captain of the New Star for the deaths of his sailors, saying he was given adequate warning.
Strong waves overturned one of liferafts after the crew fled the ship
"[He] did not take all necessary measures to fight for the survivability of his ship," it said in a statement, according to the Kommersant newspaper.
Nakhodka prosecutor Alexander Selentsov told the Interfax news agency that the captain was called by radio by border guard boats, that light signals were sent, a special flag demanding it stop was raised, and a warning shot was fired.
Interfax reported that several hundred shots had then been fired in the direction of the ship from a 30-mm automatic cannon.
Afterwards, the ship turned around but started sinking in the heavy seas, it said.
The crew then jumped into two liferafts, but strong waves overturned one of them and the border guards were only able to rescue eight men.