Juventus had called for the scudetto (title) to be revoked following allegations of involvement by Inter in the "calciopoli" corruption scandal.
The Turin team won the scudetto in 2004/05 and 2005/06 but were stripped of the titles for their involvement in the scandal and demoted to Serie B, with the latter championship handed to Inter.
"The federal council [executive committee] has turned down Juventus' petition regarding the 2006 scudetto with a declaration that it is not competent to revoke it," said the FIGC in a statement.
The FIGC explained the decision by saying that Juventus had been penalised by a disciplinary board which it did not have the power to overrule.
The decision was widely expected, coming after FIGC lawyers decided this month not to pursue Juventus's claims on the grounds that any potential charges had expired under the sporting statute of limitations.
"I would have wished for Inter to have renounced the statute of limitations," FIGC president Giancarlo Abete told reporters.
Juventus demanded the 2006 title be taken away from Inter last May after a Napoli court investigating the case heard evidence of attempts involving Inter to influence the selection of referees.
Juventus threatened to take their cause elsewhere, stating the ruling was "a long way from re-establishing fairness."
"The club has given the go ahead for its lawyers to explore the best means of proceeding in international and administrative law," the club said in a statement.
"At the same time the management and its lawyers are evaluating the economical damages such behaviour has caused."
Abete, who led the FIGC executive committee in voting 20 to one against revoking Inter's title with two abstentions, said Juventus were free to take their case to other bodies.
"I don't believe taking it to the courts would be the best choice but I'd respect the decision," said Abete. "The credibility of the system is tied to respect for the rules."
Milan, Fiorentina, Lazio and Reggina were also docked points for influencing the appointment of favoured referees in the scandal.
In May, a Napoli court ruled that Luciano Moggi, Juventus' former general manager who had been at the centre of the 2006 scandal, should face five years and eight months in jail if found guilty of corruption.
Moggi was banned for life by the FIGC last month.
Since "calciopoli" broke, Juventus, Italy's best supported club with a record 27 titles have failed to hit their previous heights, finishing outside the European places in seventh position last season.
Inter, meanwhile, have entered another golden age, winning four more titles since 2006 along with last year's Champions League and Club World championship.
Get the best features, fun and footballing frolics straight to your inbox every week.
Thank you for signing up to Four Four Two. You will receive a verification email shortly.
There was a problem. Please refresh the page and try again.