Italian state television said four of the victims were family members whose bodies were found in their flooded basement on Sunday.
Some Italian media reports put the death toll at six in Leghorn, also known in Italy as Livorno.
Mayor Filippo Nogarin said he couldn't immediately confirm the number, but added that casualties could increase because several people were missing, AP reported.
Nogarin says "a crazy amount of rain" pummeled Leghorn and "the city is literally devastated."
Train service was interrupted in parts of the Tuscan coastal area.
In Rome, which until recently suffered through 3 1/2 months of drought, the downpour made streets resemble fast-moving streams and several subway stations were closed.