Bernini, an MP for the Five Star Movement (M5S) was speaking in parliament on Wednesday, the 12th anniversary of the attacks.
He said that the official version of the event has been "proved wrong from every point of view".
"It’s clearly false and by now, the world has realized."
On 11th September 2001 terrorists hijacked four planes in the US; two crashed into New York’s World Trade Centre, another struck the Pentagon in Washington, while the fourth crashed in Pennsylvania after passengers fought against the hijackers.
But Bernini believes the account of what happened is a "conspiracy".
“We will probably never know the truth, but it is definitely completely different to the story told by mainstream media. In which case you can say that everything that you know is false and, as the American phrase goes, ‘It was an inside job’,” he said.
The 26-year-old, elected in February in the central Emilia-Romagna region, went on to elaborate on Twitter.
“If someone can show me a video where you can clearly see the plane hitting the Pentagon (the most watched place in the world)...I will resign,” Bernini wrote.
Se qualcuno mi mostra un video dove si vede bene l'aereo che colpisce il Pentagono (il luogo più sorvegliato al Mondo)... mi dimetto.— Paolo Bernini (@Paolj) September 11, 2013
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When contacted by The Local, the US embassy in Rome said it was unaware of Bernini’s statements.
Watch the video of Bernini's speech in parliament (in Italian):