Former Gen. Gary Prado allegedly exchanged "ultrasecret" encrypted e-mail with Eduardo Rozsa, a Bolivian-born Hungarian who was slain in an April 2009 raid by an elite police unit.
Authorities allege that Rozsa and two other men killed — an Irishman and an ethnic Hungarian from Romania — were involved in a conspiracy to create a separatist right-wing militia in the eastern, opposition-dominated state of Santa Cruz.
Morales said when they were killed that a plot to assassinate him had been foiled.
Prado denied having any connection with an anti-government conspiracy and said he would refuse to travel from his home in Santa Cruz, the state capital, to La Paz for questioning.
He told Fides radio Friday that his only contact with Rosza came when Rosza asked for an interview, saying he was a foreign journalist.
"What 'ultrasecret' communication did I have with Rosza, other than that interview? None," Prado said. "I did not have anything to do with that group."
Also summoned was Prado's son, who carries the same name and is running for mayor of Santa Cruz. He said the allegations were worse than a "bad soap opera."
Bolivians will elect mayors and governors across the country April 4, when the immensely popular Morales hopes to consolidate power with gains in the eastern lowlands.
Wealthy ranchers and agro-businessmen in the east oppose Morales' policy of seizing fallow lands and giving them to poor peasants from Bolivia's long-suppressed indigenous majority.
Prosecutor Marcelo Soza did not say whether authorities had been able to decrypt the e-mails he said were exchanged by the elder Prado and Rozsa, a journalist-adventurer who fought for Croatia after Yugoslavia dissolved.
Prado did not deny knowing Rozsa, who he said had approached him to inquire about his involvement in the 1967 capture of Guevara. The Argentine hero of the Cuban revolution was trying to foment an uprising in Bolivia and was later executed.
Prado, then an army captain, commanded the patrol that captured him.
The Rozsa case has major political overtones. The Morales government contends prominent opposition leaders in Santa Cruz were involved.
One of them, Branko Marinkovic, was implicated this week by a former close associate who told prosecutors Marinkovic helped fund Rozsa's group.
The accusation prompted Marinkovic, the son of Croatian immigrants, to slip out of the country. Marinkovic's lawyer denies his client's involvement in the alleged conspiracy.
Shortly after Morales' December re-election, the government confiscated land from Marinkovic.