The indictment against Castro, returned in federal court in Miami on April 23, charges him with one count of conspiracy to kill US citizens, four counts of murder and two counts of destruction of aircraft, court records show.
Five other people are also named as defendants in the case.
The charges stemmed from a 1996 incident in which Cuban jets shot down planes operated by a group of Cuban exiles, US acting Attorney General Todd Blanche said at an event in downtown Miami on Wednesday to honour victims of the incident.
"My message today is clear: the United States and President (Donald) Trump does not and will not forget its citizens," Blanche said to applause in a packed auditorium of government officials and Cuban Americans in Miami.
Castro, 94, last appeared in public in Cuba earlier this month, and there is no evidence that he has since left the island or that the government would allow him to be extradited.
The indictment comes as Trump has pushed for a regime change in Cuba, where Castro's communists have been in charge since his late brother Fidel Castro led a revolution in 1959.
Trump in a statement earlier on Wednesday called Cuba a "rogue state harbouring hostile foreign military".
"From the shores of Havana to the banks of the Panama Canal, we will drive out the forces of lawlessness and crime and foreign encroachment," Trump said at a Coast Guard Academy event in New London, Connecticut.
Cuban President Miguel Diaz-Canel said on Monday that the island does not represent a threat.
Members of Miami's large Cuban American community gathered outside the city's Freedom Tower ahead of the ceremony.
"We all hoped for a long time, for many years that this would happen," said Bobby Ramirez, a 62-year-old musician who left Cuba in 1971 when he was seven years old.
The ceremony is taking place on the anniversary of the end of a four-year US military occupation of Cuba on May 20, 1902, which itself followed centuries of Spanish colonial rule.
Cuba's government does not consider the date to mark the country's independence day, arguing that it remained subservient to the US until the 1959 revolution.
In a post on X, Diaz-Canel said that in Cuban history, May 20 signified "intervention, interference, dispossession, frustration".
Under Trump, the US has effectively imposed a blockade on Cuba by threatening sanctions on countries supplying it with fuel, triggering power outages and exacerbating its worst crisis in decades.
US Secretary of State Marco Rubio earlier on Wednesday offered Cuba $US100 million ($A140 million) in aid, and blamed Cuba's leaders for shortages of electricity, food and fuel.
Cuban Foreign Minister Bruno Rodriguez called that offer cynical, citing the "devastating effect" of the economic blockade.
