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In July 1957, a Los Angeles Times news item stated that Universal had bought the original story for Operation Petticoat from Paul King and Joseph Stone, and had assigned Gordon Kay to produce and Blake Edwards to direct "his own screenplay." The Hollywood Reporter review notes that producer Robert Arthur hired screenwriters Stanley Shapiro and Maurice Richlin to incorporate into the screenplay real-life oddities from U.S. Naval history, including the submarine operating in the Pacific called the Sea Dragon whose exposed red primer paint made it a clear target; the two native women from Tiop who gave birth aboard the U.S.S. Geta; and the torpedoing of a land bus by the U.S.S. Bowfin. The film was a co-production between Universal and the Granart Company, the independent production company owned by Arthur and star Cary Grant. According to late October 1958 Hollywood Reporter news items, Universal originally cast Jeff Chandler as "Matt T. Sherman," but then lent him to Paramount for The Jayhawkers, after which Robert Taylor was considered for the role. A December 16, 1958 Hollywood Reporter item notes that Dolores Michaels tested for a "lead" role.
A March 29, 1959 New York Times article reported the following information about the production: The ship seen in the film as the Sea Tiger was in reality the U.S.S. Balac, a World War II submarine stationed at the Key West Naval Base in Florida, where much of the picture was shot on location. Many of the sub's crew members were cast in the film, and "in compliance with an agreement of Navy cooperation at no cost to the government," the crewmen were paid by Universal to spray-paint onto the ship a temporary coat of pink vinyl. Director Blake Edwards explained in a April 12, 1959 Los Angeles Examiner article that he took some artistic license in portraying the inside of the ship, whose passageways were made four inches narrower and the steps three inches farther apart than regulation, in order to heighten the tension between the male and female characters.
According to modern sources, during the shooting of Operation Petticoat, Grant conducted an interview with entertainment reporter Joe Hyams in which he revealed that he had gained various insights from the use of L.S.D. during therapy sessions. When Hyams published his story in The New York Herald Tribune, Grant sued him, and gossip columnist Louella Parsons claimed in print that Hyams' tale was falsified. Hyams then countersued and produced a taped version of the interview, after which Grant dropped his lawsuit.
King, Stone, Shapiro and Richlin received an Academy Award nomination for Best Story and Screenplay Written Directly for the Screen. Shapiro and Richlin won the award for their other 1959 production, Universal's Pillow Talk (see below). In 1966, Bernard Newman sued the studio for $2,100,000 for plagiarism, claiming that Operation Petticoat was based on his unproduced play, A Boat for Baby. The final disposition of the lawsuit is not known. According to a July 9, 1980 New York Times article contained in the film's file at the AMPAS library, the rights to the film reverted to Grant after "six or eight years," after which he sold them to distributors N.T.A. In 1977, NBC produced a television movie version of the film that served as the pilot for a series that ran from September 4, 1977 to August 1979. The movie was written by King, Stone and Leonard Stern, and both it and the series starred John Astin as Sherman.