Morales said that "deep investigations" had determined Martinez "was in permanent contact with opposition groups".
US rejects allegations
The US state department called the move "unwarranted and unjustified".
"We reject the allegations," it said in a statement.
Last week, the Bolivian president publicly accused Martinez of "co-ordinating contacts" with a Bolivian police officer he accused of infiltrating the state oil company on behalf of the CIA.
Washington said that Morales's accusations of CIA infiltration in the country's affair were baseless and accused him of using the US as a scapegoat in domestic politics.
"We can't understand how the president can assure us that he wants better relations with the United States and at the same time continue to make false accusations,'' Denise Urs, an embassy spokeswoman, said last week.
In September, Morales expelled Philip Goldberg, the US ambassador, after accusing him of conspiracy.
Those accusations came after riots broke out in the wealthy east of the country where opposition to Morales's rule is based.
Several officials from the US drug enforcement administration have also been kicked out after being accused of espionage and of funding "criminal groups" seeking to undermine the government.
Bolivia, a close ally of Venezuela and Ecuador, had indicated earlier this month that there may be some rapprochement with the new administration in Washington, but the the latest moves are likely to further strain ties.