Interior ministry spokesman Rachid Khalfi said authorities recorded an initial "toll of 11 deaths" after "heavy thunderstorms" that hit "17 prefectures and provinces in the kingdom".
Among the victims, seven died in the province of Tata, some 740 kilometres south of Rabat, and two in Errachidia, almost 500 kilometres east of Marrakesh, according to Khalfi.
He said one of the victims had foreign citizenship, without providing further details.
Khalfi also said "the volume of precipitation recorded in two days is equivalent to that which these regions normally experience during an entire year".
The floods also caused the collapse of 40 homes and damaged 93 roads, and "affected electricity, drinking water and telephone networks", he added.
Usually arid areas in southern Morocco and Algeria have been drenched in floods caused by massive rainfall since Friday, officials told AFP Sunday.
Areas in southern Morocco have been affected "by an extremely unstable tropical air mass", the spokesman for the Moroccan General Directorate of Meteorology, Lhoussaine Youabd, told AFP.
This "led to the formation of unstable and violent clouds" that caused massive rainfall, he said, describing the phenomenon as "exceptional".
As a result, the Ouarzazate region received 47 millimetres of water in three hours, and Tagounite, near the Algerian border, some 170 millimetres, according to the Moroccan weather service.
"We haven't seen such rain for about 10 years," Omar Gana, an Ouarzazate local, told AFP.
The heavy rains hit regions of Morocco that have been suffering from drought for at least six years.
In a previous toll, Algerian civil defence said one person died in Illizi, some 1,900 kilometres south of Algiers, and one was missing in flooding in the south.
Later in the day, it gave a total of two people missing, in El Bayadh and Tamanrasset.
It also said it had rescued several families trapped by flooded rivers in the south.
Videos posted on social media showed that some areas in the Sahara desert were drenched. In Morocco's Ouarzazate, entire streets were flooded.
Morocco has been experiencing severe water stress after six consecutive years of drought, shrinking dam levels to less than 28 percent of capacity by the end of August.
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