The leftist leader yesterday said the new academy was needed to "confront the empire's cultural, ideological, political and economic domination and capitalist structure."
Morales, who has had rocky relations with the United States and expelled the US ambassador in 2008, told the inaugural class of 100 cadets that their mission would be "to defend the people, not the empire."
The head of the armed forces, General Gonzalo Duran, said the new school, located in the eastern town of Warnes, would teach about "de-colonization, gender equality, intercultural understanding and social inclusion."
Bolivia returned to democracy in 1982, after a series of coups.
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Its Cold War-era military regimes received money and training from a United States alarmed over the emergence of militant leftist movements in the region.
A country of 10 million people, Bolivia today has an army of some 46,000 troops.
The idea of an "anti-imperialist" military academy was initially proposed by late Venezuelan president Hugo Chavez, who wanted it to train officers from leftist countries around Latin America.
The new academy was born out of that project, but it will only train Bolivians.
Its alumni included top figures in some of the region's most brutal military regimes.
Originally based in Panama, it has since been renamed the Western Hemisphere Institute for Security Cooperation and transferred to Fort Benning in Georgia.