Although the ship is said to have overturned on Monday thanks to sudden, severe winds, the captain and his first engineer have both been held in police custody.
Passengers' relatives have raised questions about whether the ship should have continued its cruise after the storm started in a section of Hubei province, despite a weather warning earlier in the evening.
Heavy rains in the Yangtze area over four days from Monday have also killed 15 people and left eight others missing, the ministry of civil affairs said.
Hundreds more bodies from the Eastern Star were found overnight, bringing the death toll to 396, officials said.
The boat had more than 450 people aboard, many of them elderly tourists enjoying a cruise from Nanjing to the south-western city of Chongqing.
Fourteen people survived the capsizing, including three pulled out of air pockets in the overturned hull by divers on Tuesday.
Disaster teams placed chains around the hull and used cranes to roll the boat upright and then gradually lift it out of the currents of the Yangtze on Friday.
China's deadliest maritime disaster in recent times involved the Dashun ferry, which caught fire and capsized off Shandong province in November 1999, killing about 280 people.
The Eastern Star disaster could become the country's worst since the sinking of the SS Kiangya off Shanghai in 1948, which is believed to have killed anywhere from 2,750 to nearly 4,000 people.
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