John F. Sopko, the special inspector general for Afghanistan reconstruction, said the case began with information from an unidentified whistle-blower four years ago.

“We’ve been following this for a long time,” he said.

In all, the inspector general’s agency has won convictions of 132 people, mostly contractors in Afghanistan, as of October. Mr. Sopko asserted that corruption among American contractors has undercut efforts to fight the serious corruption problems in the country already.

“We just poured so much money into the country we contributed to the corruption problem, we were like throwing fuel on the fire,” Mr. Sopko said.

Other officials at his agency credited a 2013 article in The Wall Street Journal with prompting the investigation. The article detailed Anham’s efforts to circumvent Iranian sanctions and save on costs by shipping through Iran, and it was based on internal emails from Anham. At the time, the Pakistan border was closed and the alternative of shipping through Central Asian countries was much more costly.

According to a statement from the Department of Justice, Mr. Farouki and his co-defendants saved money on their supply contracts by shipping through Iran and then denied having done so to the Department of Defense after they became aware The Journal was about to publish its article, which also appeared based on information from a company insider. The company maintained a subcontractor was responsible, unknown to Anham’s senior managers, according to the government’s indictment.

The indictment also says that while Mr. Farouki was the company’s chief executive officer, it pretended to build warehouses required by its $8 billion “prime subsistence vendor” contract, photographed the buildings under construction to show to the government, then disassembled them.

Mr. Farouki was close to the Clintons and was a major contributor to the Clinton Foundation and other Democratic causes. He was also the chairman of the board of the American University of Afghanistan, which is funded by the United States government, until Nov. 26, according to a spokesman for the university, who suggested Mr. Farouki’s resignation had nothing to do with the Nov. 29 indictment.