In a statement posted on a government Facebook page, Madbouli said the bad weather had killed "around 20 people nationwide".
He urged local officials to declare Saturday a day off for schools and universities in order to allow the authorities to respond to the situation.
"Egypt has not witnessed such weather conditions in some 35 or 40 years," Madbouli said.
Five people died in Zaraib, south of Cairo, when their homes were swept away, a security official said earlier Friday, adding that rescue workers were looking for more victims.
In Cairo, two people were electrocuted and killed, the Akhbar el-Yom daily reported on its website.
The bad weather, forecast to continue until Saturday, was also blamed for a train crash in the capital on Thursday in which 13 people were injured.
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