Magnini and another Italian swimmer, Michele Santucci will appear before investigators in the coming days as part of a NADO probe into the work of nutritionist and doctor Guido Porcellini.
La Gazzetta dello Sport claimed that an investigation into Magnini had previously been ditched due to lack of evidence.
He was being investigated in the Porcellini affair, according to La Gazzetta, because some doping products allegedly acquired by Porcellini were reportedly destined for Magnini, but according to investigators he never used or even received them.
Porcellini, meanwhile, will appear before a court in Pesaro, Magnini's home town in the centre of Italy, on November 7.
Magnini took to Twitter immediately to play down the announcement. "I believe that the NADO probe is an obligation linked to the criminal investigation into Porcellini. Investigators have already established that I had nothing to do with this case. Let's be clear, thanks," he wrote.
Magnini, 35, was world champion in 2005 and 2007, and won bronze at the 2004 Athens Olympics with the Italian 4x200m relay team.
He is also well known in Italy as the former partner of 2008 Olympic 200m champion Federica Pellegrini, a big star in their home country.