Some reports say the dead were on a bus that slid off the ferry in Bani Suwayf region. Others say the ferry capsized.
State TV earlier put the death toll at 19 with 20 missing, while the official news agency said 43 people had died.
Transport accidents are common in Egypt, often blamed on poor maintenance and a lack of regulation.
An official told the Associated Press that the minibus had 32 passengers on board, mostly mourners heading to a funeral across the river.
The bus slid off the ferry because the emergency brake was not on, he said.
The official said 10 people had been pulled out alive, but five people were still missing.
Rescuers were at the scene, 70 miles (110km) south of Cairo, he said.
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