"USAID, with funds that come American tax payers, who think they are helping the Bolivian people, is using the money in a dirty campaign against my government and especially against me."
In February, the US said an official at its Bolivian embassy would not return to the country after being recalled following accusations of spying.
Vincent Cooper, a security adviser to the embassy, was alleged to have told a US student and several aid volunteers to pass on information about any Venezuelans or Cubans they may meet in the country.
Morales also accused USAID, which provides $85 million a year in aid to Bolivia, of attempting to stir up political opposition to him.
"The mayor of a city, who recently visited me, told me he was offered money by the US AID agency to run as an opposition congressman. They even offered to pay for his campaign.
"And the mayor told me that the people who work for the US agency go from house to house telling people that if they get rid of Evo Morales, they will have more money."
Morales, a former coca farmer, is one of a new generation of left-wing South American leaders who came to power in Venezuela, Ecuador, Argentina, Brazil and Chile.
He is also an ally of Fidel Castro, the retired Cuban leader, and a vocal critic of US foreign policy.
Morales came to power after winning 54 per cent of votes cast in an election in December 2005, becoming the first indigenous Bolivian president.
The Bolivian leader said that he had personally endured racism from opposition leaders opposed to his rule.
"As a trade union leader and leader of peasant movements, I witnessed and had to endure racism and I thought that once I was in the presidency that would stop.
"The things that some opposition groups and leaders are saying against the indigenous movement are increasingly more radical.
"For example, the governor of Santa Cruz [a Bolivian state] referred to president Hugo Chavez as the Chief Monkey, meaning that the other monkey, the other ape, was Evo Morales."
Morales is attempting to introduce a new constitution would outline a detailed bill of rights and considerable autonomy for the country's 36 indigenous groups, who say they were shut out of power by the white population.
Opposition politicians say the charter favours native communities over the rest of the population and fails to address demands for autonomy from the eastern states.
You can watch the full Al Jazeera interview with Evo Morales at 0730GMT and 1630GMT.