The country, which has the world's largest Muslim population, had a Peace Corps program briefly in the 1960s. The volunteers were assigned to train athletes for the 1964 Tokyo Olympics, which Indonesia eventually boycotted.
Theodore Friend, author of "Indonesian Destinies," told The Los Angeles Times one volunteer was assigned to edit the English versions of anti-U.S. propaganda.
Clinton, who is scheduled to be in the country Wednesday and Thursday, said during her confirmation hearings she hopes to get the Peace Corps back into Indonesia, the Times said.
Friend said Indonesian officials might view pushing the Peace Corps as condescending.
Teuku Faizasyah, a spokesman for the Foreign Ministry, said in the 1960s Indonesia and the United States had limited contact, something that is no longer true. He said there might be better ways to improve relations than bringing in the Peace Corps.
"We are not rejecting it, but we have to be clear where it's going," he said.