It sent the case back to the appeals court, ordering new trials for rail chief Mauro Moretti and another top executive, Michele Mario Elia.
A freight train carrying liquid petroleum gas derailed and exploded on June 29, 2009, while transiting through the Tuscan seaside town of Viareggio.
The force of the blast brought down two small blocks of flats where many of the victims lived, in Italy's deadliest rail accident in more than 30 years.
Rail chief Mauro Moretti, former chief executive of the defence group Leonardo, was sentenced to seven years in prison in 2017. Photo: Giuseppe Cacace/AFP
Moretti, a former boss of defence group Leonardo, was sentenced in 2017 to seven years for manslaughter and causing multiple injuries.
Elia was originally jailed for seven years and six months, although this was reduced at appeal to six years.
The court on Friday ruled the manslaughter charges had now lapsed under the statute of limitations and the new trial would only focus on allegations of negligence.
Moretti was held partly responsible for poor infrastructure and risk-avoidance systems which were deemed to have contributed to the derailing.
He was tried with around 30 other defendants, including several other state-owned railway executives.