Baggio was tasked with restoring direction to Italian football after Marcelo Lippi's World Cup holders flopped in their defence of their title at the 2010 tournament in South Africa.
The former Juventus and Inter star said the federation had shown apathy towards his plans for over a year.
"I presented my project in December 2011, 900 pages, but they remained empty words," the 45-year-old told Italian television.
"I don't like just sitting on a chair but [rather] to do things, therefore reluctantly I have decided to leave," Baggio said.
He said: "So far there has only been one successful initiative, a well-attended course in Tuscany that was free and well attended by clubs from Pisa and Pontedera."