The 29 year old was one of 50 riders implicated in last year's Operation Puerto doping scandal, which led to his exclusion from the Tour de France.
Basso's name turned up on a list of cyclists who allegedly had contact with a Spanish doctor accused of running a blood doping clinic in Madrid.
Basso was cleared of involvement by CONI and the Italian cycling federation in October.
It was not immediately clear why CONI's investigation was reopened, but the world cycling federation on Monday urged the Spanish government to do more to identify the riders involved the scandal.
Basso signed a two-year contract in November to ride for the Discovery Channel cycling team.