Ducati said in a statement that Iannone, who won in Austria in August and is joining Suzuki next season, had checks last week that showed his recovery was going well.
"However, Iannone’s doctor has advised him to continue with his rehabilitation and to wait a few more days until the fracture has completely healed, before going out onto the track once again," it added.
"The rider...in agreement with his team, has therefore decided not to take part in the GP of Japan and to return to the championship at the Australian GP from 21 to 23 October."
Ducati's only works rider in Japan will be Italian Andrea Dovizioso.
There are three races remaining after Japan. Spanish Honda rider Marc Marquez has a 52-point lead in the championship over Yamaha's Italian Valentino Rossi.
(Reporting by Alan Baldwin, editing by Ed Osmond)
