The two deserters and a third person arrested sometime earlier were accused of killing a soldier as they left a base Thursday morning.
Two of the suspects allegedly hijacked a bus to get to the Jose Marti International Airport, the Cuban Interior Ministry said in a statement, the Miami Herald reported. Among the bus passengers taken hostage was the slain soldier, the ministry said.
"Once inside the airplane, the murderers killed one of the hostages, Revolutionary Armed Forces Lt. Col. Victor Ibo Acuna Velasquez, who even though he was not armed, tried heroically to avert this terrorist act," the Interior Ministry statement said.
It also said the "effective and coordinated action of the security forces allowed the frustration of the aims of the kidnappers and the preservation of the lives of the other hostages."
The statement blamed the attempted hijacking on U.S. policies, the Herald reported.
It was the first plane hijacking attempt in Cuba since March 2003, when two separate craft were commandeered by hijackers and one was flown to nearby Key West, Fla.