Lord says the university is cooperating with law enforcement.
He says the alleged embezzlement was discovered by an internal investigation launched after a tip from the FBI.
An FBI spokesman declined to comment on whether the agency is investigating.
Lord says two other employees were fired for allegedly failing to establish proper controls but that neither is suspected of wrongdoing.
Naropa was founded in 1974. Its teachers have included poets Allen Ginsberg and Anne Waldman and composer John Cage.
