On Thursday morning, Iraqi medical sources said the tally of bodies recovered from the Tigris had risen to 60.
Earlier, President Jalal Talabani said the discovery proved that armed Sunni fighters had seized up to 100 Shia last week in the town of al-Madain, 20km southeast of Baghdad.
But local officials said the bodies had been floating to the surface for weeks, and there was no way of telling where they came from.
Iraq was last week rocked by claims that fighters had seized as many as 100 Shia Muslims and were threatening to kill them unless all Shia left the area.
"Terrorists committed crimes there. It is not true to say there were no hostages"
Shia leaders and government officials warned of a major sectarian standoff, only to see the claims evaporate when Iraqi security forces swept into the region over the weekend and found no hostages.
But Talabani said he knew where the bodies found in the Tigris came from.
"Terrorists committed crimes there. It is not true to say there were no hostages," he said.
But Dr Falah al-Parmani, head of the Suwayra health department, said families had identified just a few of the bodies, and it was impossible to tell where most were from.
"The extent of decomposition suggests all the slayings happened more than three weeks ago, while the crisis in al-Madain started less than one week ago," al-Parmani said.
"So there is no way to link the two incidents."
He said the entire region had seen a surge in hostage-takings in recent months, which could account for the bodies. Some of the abductions were sectarian in nature.