Investigators concluded that Seeger's association with known communists and his Japanese-American fiancee pointed to a risk of divided loyalty.
Seeger's "Communistic sympathies, his unsatisfactory relations with landlords and his numerous Communist and otherwise undesirable friends, make him unfit for a position of trust or responsibility," according to a military intelligence report.
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The investigation, forwarded to FBI Director J. Edgar Hoover, is detailed in more than 1,700 pages from Seeger's FBI file, released by the National Archives under the Freedom of Information Act.
The musician and left-wing activist known for such songs as "If I Had a Hammer," ''Where Have All the Flowers Gone" and "Turn, Turn, Turn" died in January 2014 at age 94.
The government's interest in Seeger is no surprise. He was a member of the Communist Party for a period of time, as he later acknowledged, saying he quit around 1950, and he performed with Guthrie and others in the proudly leftist Almanac Singers before he was drafted.
But the newly released files show the lengths to which the government went to keep tabs on the singer's travels, performances and rally appearances at least into the 1970s. The archives plan to release additional Seeger files in the future.
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The degree to which the security investigation affected his military career is not spelled out in the files. Seeger trained as an airplane mechanic at Keesler Field in Mississippi and, according to his file, expressed frustration that he was being kept stateside instead of being sent to where the fighting was. Ultimately, the singer and banjo player spent time in the Special Services, entertaining soldiers in the South Pacific, and made corporal.
Based on these records, Seeger underwent what appears to be his first major investigation after writing a letter to the California American Legion in 1942 criticizing the organization's resolution "advocating deportation of all Japanese, citizens or not, and barring all Japanese descendants from citizenship." This was during a time Japanese-Americans, many of them from California, were being forced to live in government internment camps.
"We're fighting precisely to free the world of such Hitlerism, such narrow jingoism," Seeger wrote.
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What followed was a wide-ranging probe by the military into Seeger's background. Investigators found that Seeger -- referred to as the "Subject" -- was "intensely loyal at this time" and eager to be transferred overseas from Mississippi to fight fascism.
But they didn't like the company he kept.
Investigators found Seeger was a "close friend and associate" of Lead Belly, or Huddie William Ledbetter, the folk legend they described as a "negro murderer." The Almanac singers were described in the files as "spreading Communist and anti-Fascist propaganda through songs and recordings."
Guthrie told an investigator that his buddy was "brilliant, but he was hard to understand," always trying to make things run more efficiently. The agent concluded Guthrie was telling the truth "but that he knew a great deal more about Subject's politics and activities than he admitted."
They also uncovered evidence Seeger was not a good tenant. A New York City landlord complained to an investigator that she had rented a one-person basement apartment to Seeger, but the next day a fellow named Guthrie turned up and never left. Then a woman they claimed was a sister showed up. Frequent callers included a group of "disreputable" and "noisy" men who wore lumber jackets and blue denim trousers and carried guitars.
"She was glad when they had left," though she was stiffed a half-month's rent, the agent wrote.
As the military built its case, Seeger held out hope that he would get to fight overseas. In Mississippi, Seeger wrote to his wife-to-be, Toshi, in New York City about a conversation with two "progressives" at camp.
"These two think that the reason I'm staying here so long is because of the Almanacs and you, but I really don't think so -- not for another month or so. (Funny that's what I said last month, isn't it?)," he wrote.
Toshi worried that she was, in fact, part of the reason he was being kept from going overseas.
Months before the couple's wedding in 1943, Toshi wrote in an intercepted letter that in one sense she didn't mind him avoiding danger overseas -- though she hinted that there might be perils stateside, too.
"In the future I would be a little careful what you put in letters," she wrote. "But put plenty of love in them."