The second program, called the Article 2 Fund, compensates survivors who lived in hiding, under a false identity, in a Jewish ghetto, or who were incarcerated in a labor or a concentration camp. This program provides monthly payments of approximately $411 to survivors who make less than $16,000 per year.

“The alleged fraud is as substantial as it is galling,” Mr. Bharara said at a news conference announcing the indictment. The charges followed a yearlong investigation by the Federal Bureau of Investigation. F.B.I. agents arrested 11 of the defendants Tuesday morning; 5 were previously charged.

The suspects are each accused of playing a role in creating, filing and processing fraudulent claims on behalf of applicants who should not have qualified for compensation. Semen Domnitser, who was the director of the Hardship and Article 2 Funds until he was fired on Feb. 3, was accused of being the leader. At the fund, his responsibilities included reviewing all applications for approval before they were sent to Germany.

The claims conference became suspicious when employees noticed two applications that came in within two weeks that had remarkably similar facts, said Gregory Schneider, the executive vice president of the organization. They began to look for patterns and, after finding other problems, alerted the F.B.I. in December 2009.

To date, investigators have found nearly 5,000 false applications from 2000 through 2009 to the Hardship Fund, resulting in a loss of about $18 million. They have found 658 fraudulent applications to the second fund, from 1993 to 2009, with losses of about $24.5 million.

Mr. Schneider said the theft amounted to less than 1 percent of the claims filed since the two programs’ inception. He said his organization had processed 630,000 applications for the two programs over the last two decades. He said he suspected that the nearly 6,000 people involved in the false claims were a mix of those who were aware they were committing fraud and those who may have been used.

When Mr. Bharara was asked whether the thousands of others involved in the fraud could be charged, he said, “the investigation remains open.”