Six other crew members were plucked from choppy seas by marine police shortly after their 75m long barge overturned, throwing them into the sea east of the island at about 3.15am.
The six crew feared dead on the barge were asleep in their bunks when the collision happened.
Last night an air and sea search and rescue operation was still under way for the six missing crew – five men and one woman. The Director of Marine has ordered an investigation.
The Runz 001 barge was travelling through Hong Kong waters on its way from Fu Yong, in western Shenzhen, eastwards to Yan Tian in Mirs Bay, with a crew of 14 mainlanders – 13 men and one woman.
The nine crew members on the 50m cargo ship, Hui Jin Qiao 08, were unhurt in the collision. The vessel was taken to the Chai Wan public cargo working area.
The cargo ship was supposed to be heading east at the time, having left Tsing Yi at 11pm on Monday and heading to Shantou in eastern Guangdong province.
But the ship was heading south when the collision with the barge occurred, a government official said. The Marine Department is investigating why it was heading south.
"The route and direction were not the cause of the accident," the official said. "It [is considered] open sea and there is no fixed shipping channel."
The barge capsized after the collision and drifted 500m to the southeast before sinking, about five hours later, in 22m of water.
Seven men were plucked from the water by marine police, none wearing life jackets. Six of them were conscious and the seventh, the 50-year-old captain of the barge, was unconscious and later died in hospital.
At about 12.20pm, another body was recovered west of the island.
"The missing crew members were probably asleep in the rooms on the first floor of the three-storey control tower of the barge at the time the collision occurred," a fire officer said.