Chavez, who led Venezuela for 14 years, died at age 58 after a two-year-long fight against cancer.
Nicolas Maduro, who was vice president under Chavez and was sworn in as acting president, earlier accused Venezuela's enemies of causing Chavez's cancer.
He said the issue would be investigated by a special commission.
Morales, who travelled to Caracas to attend Chavez's state funeral, said he had always been aware of Chavez's disease although he never revealed any details.
Morales recalled he had once offered Chavez some coffee but the Venezuelan leader's security guards objected.
"Brother Chavez said (to his guards): 'How can you think that Evo will poison me?' and then he had coffee," the Bolivian president said.
Morales did not elaborate what "the empire" meant.
Chavez's funeral was attended by over 30 heads of state and government.
Venezuela will hold presidential elections April 14 to elect a successor to Chavez.
Caracas: Bolivian President Evo Morales has said he is "almost certain" that "the empire" had poisoned the late Venezuelan leader Hugo Chavez.
First Published: Sunday, March 10, 2013, 13:31