Paolo Gentiloni made the controversial comments at the end of a two-day EU summit where leaders finally agreed Brexit talks could move on to trade.
In a press conference, Mr Gentiloni hit out at Germany over the way Italy was treated in its bid to be the new home of the European Medicines Agency (EMA), currently based in London.
Milan narrowly lost out to Amsterdam after votes were left deadlocked in last month’s decision – leading to straws being drawn to decide.
And the Italian premier placed the blame firmly at German Chancellor Angela Merkel’s door.
He said: “Regarding the EMA, Italy has made a good impression despite that misfortune.
“Between the 27 European countries, Italy was the country that had more support.
“However, that is not the right way the measure the power of a country.
“If not, Italy would be a super power and Germany would be a disaster.”
The EMA is responsible for the scientific evaluation, supervision and safety monitoring of medicines in the bloc and is seen as a prestigious institution.
But the prime minister also claimed Italy was very “stable” and asked why it was compared to politically-stalled Germany.
He said: “If you look at the 27 EU countries, many majorities are fragile, there are governments on hold. “Given the stability of European governments, which shouldn’t alarm anyone, Italy is not so bad.
“People talk about the stability of Italy, like they talk of the stability in Germany or Catalonia.”
In the same press conference, he warned Theresa May against trying to “cherry-pick” EU perks like the single market in her final Brexit deal.
EU President Donald Tusk warned it would be “dramatically difficult” to get both a withdrawal deal and an agreement on a future trade relationship done by Brexit day on March 29 2019.
He said: ”It is still realistic and of course dramatically difficult.
“For sure, the second phase will be more demanding, more challenging than the first phase.”