The European Union and Canada formally signed the Comprehensive Economic and Trade Agreement (CETA) in October 2016, at a time when anti-globalisation sentiment was on the rise in Europe.
The accord, which has yet to be ratified, eliminates 98 percent of tariffs between the EU and Canada.
Opponents to the accord from around Europe see it as a danger to health, democracy and the rule of law.
Farmers in Italy protested in 2017, demanding that the government refuse to ratify the pact.
CETA's supporters, however, see it as an extension of the global trade system that faces a threat from protectionist US President Donald Trump.
The global system has also come under attack from eurosceptics and anti-establishment parties like those swept to power in Italy in a March vote.
In an interview published in Italian daily La Stampa on Thursday, Agriculture Minister Gian Marco Centinaio said: "We will not ratify the free-trade agreement with Canada because it only protects a small part of our protected designation of origin (PDO) and protected geographical indication (PGI) produce."
He added: "We will ask parliament not to ratify this treaty or others similar to CETA."
Centinaio said the decision was covered in the joint government contract published by the populist coalition government made up of the anti-establishment Five Star Movement and the far-right League
Centinaio, a League member, said that his decision did not reflect just the nationalist position of his party, but that "doubts over this agreement are common among my European colleagues".
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