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According to documents in the Twentieth Century-Fox Records of the Legal Department and the Twentieth Century-Fox Produced Scripts Collection at the UCLA Arts-Special Collections Library, Down to the Sea in Ships was a project which studio head Darryl F. Zanuck had long wanted to produce. In 1940, Zanuck announced that the studio was producing "three films of the 'road-show' variety...Lillian Russell, Brigham Young and Down to the Sea in Ships." At that time, the studio had acquired an option on the rights to a 1923 film titled Down to the Sea in Ships made by the Whaling Film Corporation of New Bedford, MA. However, the film that was eventually produced by Zanuck was not a remake of the 1923 picture but was based on a new story. October 1940 Hollywood Reporter news items reported that Tyrone Power and Laird Cregar would star and that the studio had sent a crew, headed by James Havens, to Mexico to film whaling operations. However, because of wartime restrictions, the film was shelved for several years. In a September 1945 Hollywood Reporter news item, the studio announced a revival of the project with Power still being considered for the lead. At that time, however, there was no completed screenplay, and writer Sy Bartlett did not become involved in the project until mid-1946. In a February 1948 memo to producer Louis D. Lighton, Zanuck expressed dismay at the length of the 178-page script and proceeded to make radical cuts in it in order to reduce production costs
The majority of the film was shot on one sound stage, in which a full scale reproduction of a whaling ship was built on a hydraulically moveable cradle so that it could be made to sway in front of the sea backgrounds, which were projected on process screens. A few shots were done in waters off Seal Beach, CA but most of the action involving the harpoon boats was done in the studio tank. An April 1949 American Cinematographer article details the shooting of miniatures for the collision of the ship and the iceberg. A studio press release contained in the AMPAS Library files reported that the studio bought four tons of whale blubber from a whaling company in Vancouver, shipped it to the studio in refrigerated trucks and kept it frozen until it was used for the rendering sequence.
Studio records indicate that scenes involving actors Ruth Donnelly, Connie Marshall and Hubert E. Flanagan, as neighbors of Captain Joy in New Bedford, were shot but cut from the film before release. Other legal records list Harry Carter and Bob Adler as members of the ship's crew, but their appearance in the released film has not been confirmed. Studio records also indicate that one of the film's art directors, Ben Hayne, and technical advisor Albert C. Wilvers appeared in the film. Lionel Barrymore and Dean Stockwell were borrowed from M-G-M for this film, which also marked Richard Widmark's first sympathetic role. Widmark appeared at the film's elaborate three-theater, world premiere in New Bedford and rejoined Barrymore for a radio adaptation of the film broadcast on Lux Radio Theatre on April 30, 1951.