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The title credit reads "Carol Reed's production Our Man in Havana." In the film's opening shot, an attractive woman swims in a pool as "Capt. Segura" watches her. The camera then cuts to a man gazing at a seductive woman standing on a balcony. The following written prologue appears over the image of the woman swimming in the pool: "This film is set in Cuba before the recent revolution." According to a Hollywood Reporter item in the "Rambling Reporter" column, the decision to film in Havana was made in December 1958. On January 1, 1959, Fulgencio Batista, the head of Cuba's U.S.-backed regime, was ousted from power by a military junta, and on February 16, 1959, Fidel Castro was appointed prime minister of the newly installed revolutionary government (for more information about Castro and the Cuban revolution, please for The Truth About Fidel Castro).
An April 1959 New York Times article noted that the regime change meant that the film's script had to be submitted to the Minister of the Interior, which suggested thirty-nine changes. The New York Times added that establishing the film took place before the revolution would avoid any criticism about presenting the current regime as corrupt. According to a January 1959 news item in Los Angeles Times, the character of Capt. Segura was modeled on Capt. Esteban Bentura, the head of Batista's police squad. A May 1959 Variety article noted that the Cuban labor union insisted that British production personnel were matched by Cuban stand-bys.
The Variety article added that filming in Cuba presented several obstacles. The noise of Cuba's streets required that the soundtrack be post-recorded at a local studio at the end of each working day. Daily rushes were sent to editor Bert Bates in London, creating a three-day delay between the time the footage was shot and Bert's viewing of the results and reporting back to Reed. An April 1959 article in Time added that location shooting was done at the Havana Biltmore Yacht and Country Club and other locations in Havana. According to October and December 1958 Hollywood Reporter news items, Jean Seberg and Evy Norland were considered for the role of "Milly." In February 1959, Daily Variety reported that Lauren Bacall was being considered for a role.
The film closely parallels Graham Greene's novel. The major differences are that "Professor Sanchez" has a larger role in the novel, which ends with "Wormold" being given a second assignment. Lambs' Tales, originally known as Tales from Shakespeare which figures prominently in the film, was an 1807 compendium of summaries of William Shakespeare's plays written by Charles and Mary Lamb. A biography of Reed noted that Greene worked as a spy in the British Secret Service from 1943-1944. Fifteen years before writing the novel, Greene conceived of the idea for Our Man in Havana in an outline he wrote for Brazilian filmmaker Alberto Cavalcanti. The plot was originally set in Estonia during World War II, and Cavalcanti and Greene were forced to abandon the project when the British Board of Film Censors refused to issue a certificate because the film would make fun of the Secret Service. Fifteen years later, Greene wrote the novel, but changed the setting to Cuba because he felt that "a reader would not be sympathetic to a man cheating his country in Hitler's day." The biography noted that Alfred Hitchcock negotiated for the screen rights to the novel, but would not meet Greene's price.
Reed, who directed two other films based on Greene novels, The Third Man and The Fallen Idol, then secured the screen rights. Kingsmead Productions, the company that produced Our Man in Havana, was organized by Reed. The film was made with the financial backing of Columbia Pictures. Although the Variety review says that local music was "composed by Hermanos Deniz and played by his Cuban Rhythm Orchestra," Filmfacts calls it "The H. Deniz Cuban Rhythm Band."