The pope appealed to Castro "as soon as he heard about the news of the heavy sentences inflicted on a significant group of Cuban dissidents, three of whom were sentenced to death," a Vatican statement said.
The appeal, dated April 13 but released only Saturday by the Vatican press office, was made through the Vatican secretary of state, Cardinal Angelo Sodano.
The pope expressed "profound pain" over the recent firing-squad executions of three hijackers of a ferry boat and "deep sorrow" over the long prison sentences handed out to 75 dissidents, "asking President Fidel Castro for a significant gesture of clemency toward those convicted," the Vatican said.
The dissidents were sentenced after quick trials to prison terms ranging from six to 28 years on charges of collaborating with American diplomats to subvert the island nation's socialist system.
The convicted dissidents and the diplomats have denied the charges, and the sentences were criticized internationally.
The pope's letter, dated April 13 but released only Saturday by the Vatican press office, began with Easter greetings to the traditionally Catholic nation.
"The Holy Father has felt deeply pained when he learned of the harsh sentences recently imposed on numerous Cuban citizens, and, even, for some of them, the death penalty," Sodano wrote in Spanish.
"In the face of these facts, His Holiness charged me with asking Your Excellency to give full consideration to a significant gesture of clemency toward those convicted, with the assurance of knowing that such an act will contribute to create a climate of greater detente to the benefit of the dear Cuban people."
John Paul, the first pope to visit Cuba with his 1998 pilgrimage, staunchly opposes the death penalty.
"I am sure that you also share with me the conviction that only a sincere and constructive confrontation between the citizens and the civil authorities can guarantee the promotion of a modern and democratic Cuba ever more united and fraternal," Sodano concluded, closing by expressing to Castro "my highest and most distinguished consideration."
The Vatican's press office was closed for the day, and officials could not immediately be reached for elaboration, but the Holy See, in its introduction to the letter's text, seemed to be taking a significant stand by describing the hijackers as dissidents and not criminals.
No one was hurt in the April 2 hijacking of the ferry Baragua. The men, armed with at least one pistol and several knives, seized the ferry in Havana Bay and set sail for the United States with about 50 hostages on board.
Later that day, the ferry ran out of fuel in the high seas of the Florida Straits after being chased by two Cuban Coast Guard patrol boats.
The hijackers allegedly threatened to throw passengers overboard but eventually agreed to let the ferry be towed the 30 miles back to Cuba's Mariel port for refueling.
After the boat was docked in Mariel, west of Havana, Cuban authorities stormed the ferry and arrested the suspects.
The ferry was hijacked a day after a man who said he had two grenades forced a Cuban passenger plane to fly to Key West, Fla. The grenades turned out to be fake.