The novel provides a good answer to this question. After the Japanese attack on Pearl Harbor, a United States navy base, the narrator Jeanne reports that the American government was suddenly fearful of Japanese people who owned commercial fishing licenses (or even radios). Through its FBI agents, the United States government began taking these men into custody for questioning and detention. Though it seems outlandish now, at the time, Americans were afraid that Japanese people living in the United States would display their loyalty to the Japanese emperor and would sabotage the war effort by communicating with enemy Japanese ships or planes.
Japanese-born men like Jeanne's father were suddenly perceived with suspicion by American citizens, who viewed them as men "with no rights who looked exactly like the enemy." Even Japanese-American children born here, like Jeanne, were treated with icy reserve by American citizens: the young girl's teacher maintained a...
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cold distance from Jeanne, refusing to help her or even speak with her when Jeanne was struggling to keep up with her schoolwork.
In Chapter 2, the narrator explains all this hostility directly: "Tolerance had turned to distrust and irrational fear." She describes how her older siblings heard about attacks on Japanese homes and public violent eruptions toward Japanese citizens.
In short, the Japanese attack on American soil caused American citizens to extend a deep distrust and hostility toward United States residents of Japanese descent.
How does the Pearl Harbor attack create anti-Japanese feelings in Farewell to Manzanar?
The attack on Pearl Harbor made many people hate and fear Japanese-Americans, worrying that they might be spies for Japan.
The attack on Pearl Harbor by Japanese forces was the first attack on American soil in a very long time. It made people very angry and they took out their anger on Japanese Americans. Jeanne and her family have no idea what Pearl Harbor is. They have never heard of it, and until the Japanese bomb it, Pearl Harbor has no meaning to them.
That night, her father burns his Japanese flag and all papers that might show he has ties with Japan. As Jeanne noted, the “precautions” did not help. Her father was a target.
He was not only an alien; he held a commercial fishing license, and in the early days of the war the FBI was picking up all such men, for fear they were somehow making contact with enemy ships off the coast. (ch 1, p. 7)
So though the family had no Japanese military connections anymore and no involvement in Pearl Harbor, they lost everything. The American government rounded them up and stuck them in an Internment Camp, to protect America from them until the war with Japan ended.