Mercosur, principally a trade bloc, has ambitions to transform itself into an EU-style regional alliance but increasingly faces members failing to match the rhetoric with actions and opting, instead, for bilateral deals within and outside Latin America.
Humala is the first Latin American leader to spell out reluctance to join Mercosur in recent years. Business leaders in Venezuela, a full member waiting for accession, voiced opposition to the country joining the trade bloc, arguing it was too weak to withstand regional trade competition.
Mercosur, founded in 1991, includes Argentina, Brazil, Paraguay and Uruguay as full members and Bolivia, Chile, Colombia, Ecuador and Peru as associates.
Mercosur is seeking a trade pact with the European Union but is facing resistance from European lobbyists concerned over unfair competition from Latin America's cheaper exports.
Humala said he regarded full membership of Mercosur as a distant possibility.
Part of the reason for Peru's reluctance, he indicated, was the presence of competing free trade agreements with other countries.
"We want to build on a positive regional agenda based on integration but full membership of Mercosur is distant because Peru has at least 10 free trade agreements with other countries and that means tariff problems, which can't be overcome in the short term," Humala said at a news conference in Montevideo, Uruguay, during a short visit and talks with President Jose Mujica.
Instead, Humala said, he would seek to build Mercosur links in security and counter-narcotics cooperation and even education.
Humala came to power in an April election, succeeding Alan Garcia. He campaigned as a center-left politician with the declared aim to create a more equitable system for income distribution and sharing of wealth from the country's natural resources.
Humala said he would seek to build closer relations with all Mercosur member states with the aim of improving Peru's economy and attracting more foreign investment.
He also left the door open for political reconciliation and hinted he would consider pardon for former President Alberto Fujimori, currently serving a 25-year sentence on charges of corruption and human rights violations.
Humala narrowly defeated Keiko Fujimori, daughter of the imprisoned Fujimori, in the election. He will be sworn in July 29 as the president and will serve a term of five years.
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