Mubarak was quoted as telling editors of state-run Egyptian newspapers on Thursday that hanging the former Iraqi leader would lead to more sectarian strife in Iraq.
He said: "Carrying out this verdict will explode violence like waterfalls in Iraq.
"The verdict will transform [Iraq] into blood pools and lead to a deepening of the sectarian and ethnic conflicts."
The strong comment by Mubarak, a regional heavyweight and a top US ally, came amid mixed reactions among Arabs on Saddam's death sentence.
While some rejoiced at Saddam being removed from power after the US-led invasion, spiralling violence in Iraq and the unprecedented step of sentencing an Arab ruler has since created growing unease in the region.
Leaders in neighbouring Saudi Arabia, another regional powerhouse and US ally, have remained largely quiet about Saddam since his sentencing.
The presidents of Libya and Syria have also avoided commenting on the verdict.
An Iraqi court sentenced Saddam on Sunday to hang for the deaths of about 150 Shias following an assassination attempt against him in 1982 in the town of Dujail.
Saddam has appealed, and is being separately tried for genocide in the deaths of about 180,000 Iraqi Kurds, mostly civilians, during a crackdown against Kurdish fighters in the late 1980s.