The colonel died, when two army deserters, who were attempting to hijack a passenger plane, shot him at the domestic terminal of the Cuban airport early Thursday. The hijackers were arrested.
"The crime was possible thanks to an American law that automatically grants Cubans, who find themselves on American soil, refugee status," the Interior Ministry said in a statement Friday.
"The U.S. authorities are responsible for a new crime in a long list of terrorist acts committed against Cuba over the past 50 years," the ministry said.
The soldiers, who served at a base in Managua, about 30 km (about 18.6 miles) south of Havana, had been on the run since April 29. They seized a bus with several passengers and drove it to the terminal.
The deserters ordered the hostages to move to a nearby empty plane and shot the officer as he tried to stop the hijacking. They were subsequently captured by security forces, the ministry said.
"Decisive action allowed security forces to prevent their escape and release the hostages," the ministry said.
In April, a man armed with a hand grenade hijacked a plane with 40 passengers onboard demanding he be taken to Key West, Florida.