Castro himself was seen arriving at the scene of the hijacking drama at Mariel port shortly before the government announced on state television that the boat and the hostages were still be held hostage.
"Force will be used if the hostages' situation becomes critical," warned a statement read on the midday broadcast.
"All morning long over the radio an effort has been made to persuade them to free their hostages," said the statement. "After repeated exhortations, they only agreed to turn over three: two women and a man with health problems. To all other requests they have responded only with their demands for fuel."
The Cuban government earlier had said there were an estimated 50 people aboard the ferry when it was hijacked in the early hours of Wednesday from Havana Bay and sailed northward toward the United States.
The ferry returned to Cuba late Wednesday in search of fuel after Cuban authorities chased it some 30 miles into international waters.
Early Thursday, the ferry could be seen docked inside the free trade zone at Mariel. Authorities blocked access to international journalists, but several dozen officials, a fire truck and numerous government vehicles could be seen near the boat from a hill high above the bay.
When the ferry was still in the middle of the Florida Straits, FBI agents had waited nearby on a U.S. Coast Guard cutter as Cuban authorities tried to persuade the hijackers to give up. The men had threatened to throw some of the passengers overboard if they did not get their way, Cuban authorities said Wednesday.
As the boxy, flat-bottomed ferry struggled through choppy seas on Wednesday, the hijackers had radioed a command post of the Cuban coast guard to demand another boat and enough fuel to reach the United States, Cuba's Prensa Latina news service said.
The seizing of the vessel came a day after a Cuban passenger plane was hijacked to Key West, Florida, by a man who allegedly threatened to blow up the aircraft with two grenades that later turned out to be fake. Another Cuban plane was hijacked to Key West less than two weeks before.
The string of hijackings coincides with a new crackdown on dissent in Cuba and rising tensions with the United States. Trials began Thursday for the first of 80 dissidents on charges of conspiring with U.S. officials.
In the past, Cubans have taken advantage of periods of U.S.-Cuban friction to try to flee the island.
Earlier, an FBI spokeswoman in Miami said that agency negotiators flown by helicopter to the scene of the ferry standoff stood by on the Coast Guard cutter while Cuban authorities dealt with the situation. The ferry at the time was drifting in international waters about 60 miles off Key West, she said.
The cooperation between agencies from both countries underscored the worries both American and Cuban officials have about the recent rash of hijackings.
In a highly unusual move, the top U.S. diplomat in Havana on Wednesday night warned Cubans not to undertake any more hijackings, telling them in a message read on communist-run television that they would be prosecuted by U.S. authorities and lose the right to seek American residency.
The message by James Cason, chief of the U.S. Interests Section, demonstrated growing worries about the possibility that such hijackings could end in violence or spark a migration crisis.
The high seas drama began early Wednesday when a group of people armed with three pistols and at least one knife hijacked the ferry, Cuban authorities said.
The ferry provides service between Havana and the small communities of Casablanca and Regla on the other side of Havana Bay.
Several ferry boats were hijacked to the United States in 1994, when some 35,000 Cubans headed toward Florida in dilapidated boats and rafts. The wave of illegal migrants subsided only after the United States agreed to send back Cubans picked up at sea.