According to the Guardian, the decision to forbid the filming of the Morgan Freeman and Jack Huston version of 1959 Charlton Heston film was made by the Italian culture ministry for "technical" reasons".
However, commentators believe last year's row over a decision to allow the Circus Maximus play host to 65,000 Rolling Stones music fans on the "very fragile" site was also behind the ban on filming at the location.
Rome's mayor, Ignazio Marino has described the ban, which had already been given the green light by local authorities as a missed opportunity, he said: "The aim of the city administration isn't so much to raise revenue in exchange for the use of public space, but to give back to Rome the role of being a big international set, which is in our history and our tradition".
The Ben-Hur remake, starring Jack Huston as Judah Ben-Hur, will still be filmed in Italy, at a special stage built at Rome's Cinecitta studios, a 100-acre facility that has languished for decades from its high in the 1960s, when it was known as Hollywood on the Tiber.
The studio is seeking to bring in new revenue following the introduction last year of 25% tax breaks for foreign film productions.
The film's due out next year.