Italy is the only Group of Eight industrialized nation that does not produce nuclear power, but Prime Minister Silvio Berlusconi wants nuclear plants to generate a quarter of the country's electricity in the future.
The court allowed a request by opposition politician Antonio Di Pietro for a referendum, which will take place between April 15 and June 15.
Public opinion in Italy has been generally hostile to nuclear energy, and a 1987 referendum following the Chernobyl disaster in Ukraine in 1986 closed all plants and phased out production.
Italy's biggest utility, Enel, now has plans to start building nuclear power stations in the country together with French power giant EDF in 2013.
In November, Italy set up a new nuclear safety agency, which industry participants expect will define the precise criteria for selecting sites for nuclear power stations and oversee their construction and operation.
The court also ruled that two referendums against water sector reform plans could go ahead.
Italy aims to attract private investments in the billions of euros to boost water supplies and upgrade transport, sewage and water treatment systems. Opponents of water sector reform say it would amount to privatization of a precious national resource.