Agee, 72, died on Monday night, the newspaper said, calling him a "loyal friend of Cuba and staunch defender of the people's struggle for a better world."
His widow, German ballet dancer Giselle Roberge, told friends he had been in hospital since December 15 and did not survive surgery for perforated ulcers.
Agee worked for the Central Intelligence Agency for 12 years in Washington, Ecuador, Uruguay and Mexico. He resigned in 1968 in disagreement with U.S. support for military dictatorships in Latin America and became one of the first to blow the whistle on the CIA's activities around the world.
His book "Inside the Company: CIA Diary" revealed the names of agents in Latin America and was published in 27 languages.
Agee said working as a case officer in South America opened his eyes to the CIA's Cold War goal in the region: to prop up traditional elites against perceived leftist threats through political repression and torture.
"It was a time in the 70s when the worst imaginable horrors were going on in Latin America -- Argentina, Brazil, Chile, Uruguay, Paraguay, Guatemala, El Salvador -- they were military dictatorships with death squads, all with the backing of the CIA and the U.S. government," he wrote.
"That was what motivated me to name all the names and work with journalists who were interested in knowing just who the CIA were in their countries," he said.
The U.S. government called him a traitor and said some of the agents he exposed were later murdered, an allegation Agee rejected.
Agee went to live in London but was deported by Britain in 1976 at the request of then secretary of state Henry Kissinger. The U.S. government revoked his passport three years later.
Barbara Bush, the wife of former U.S. president George Bush, who was CIA director in 1976, blamed Agee in her memoirs for the murder of the Athens station chief, Richard Welsh, in 1975. Agee denied any connection and sued her for $4 million, forcing her to revise the book to settle the libel case.
Agee, a German citizen through marriage, settled in Cuba in the 1980s after several European countries denied him residence.
In 2000, Agee set up an online travel agency catering to Americans willing to defy a U.S. travel ban and visit the Communist-run island. The business folded due to tighter enforcement of sanctions by President George W. Bush.
© Reuters 2008