New Orleans — Elton “Mark’’ McCabe, the Slidell businessman who returned to the United States on Monday after two month’s imprisonment in South Sudan, is now facing charges in this country that he took tens of thousands of dollars in kickbacks while he was working in Afghanistan in 2009.

A South Sudanese court threw out all charges against him earlier this month, and McCabe flew into Louis Armstrong International Airport on Monday, where he was greeted by family and reporters who had been following the story of his detention and efforts by his wife, Anne, and Sen. David Vitter to secure his release.

But on Thursday, a criminal complaint filed in U.S. District Court in the Eastern District of Louisiana was unsealed that charges McCabe with one count of receiving illegal kickbacks and one count of wire fraud.

Mark McCabe, reached at his Slidell home, declined to comment but put Anne McCabe on the phone. “Those are allegations that he has to show proof are false,’’ she said.

She said that the only notification that they had received concerning the federal charges came in an email that was sent when her husband was still imprisoned in South Sudan.

According to court documents, McCabe worked for a construction company that received subcontracts from prime contractors to the U.S. government for reconstruction efforts in Kandahar, Afghanistan.

In mid- to late 2009, McCabe allegedly solicited and accepted cash payments and a wire transfer of approximately $53,000 to his wife’s bank account from subcontractors in exchange for awarding subcontracts in connection with U.S. reconstruction projects in Kandahar, according to a Justice Department news release.

McCabe is also alleged to have accepted cash payments and arranged for a contractor’s consultant to wire $20,000 to McCabe’s wife’s bank account in exchange for construction material that belonged to McCabe’s company and that McCabe did not have the authority to sell for his personal benefit, the Justice Department said.

According to court documents, McCabe used the alleged kickbacks he received from subcontractors to pay for personal family expenses.

Anne McCabe said that her husband worked for about six months for the construction company, which she said is owned by a woman named Sara Lee. Anne McCabe said that the government is using her husband as a witness. “You know, when you’re in bad company,’’ she said.

“He has to get an attorney to represent him to clear up anything she (his former boss) might have said,’’ she said.

Vitter, who wrote several letters to the South Sudan government on McCabe’s behalf, could not be reached for comment. But his spokesman, Luke Bolar, said, “Sen. Vitter believes that if these extremely serious charges are true ... Mr. McCabe should suffer a harsh penalty. Of course this is very different than Mr. McCabe being thrown in jail by South Sudanese security forces without evidence, and being denied medication for his very serious heart condition.”

McCabe, who went to work in South Sudan in August, was seized by that country’s National Security Service in mid-October. According to his wife, he was falsely accused, along with his Iraqi business partner, of trying to abduct an Indian businessman. He was held for nearly two months before he was finally released from prison after a hearing on Nov. 22. When he arrived in New Orleans on Monday, he said that he had been held in four different prisons and never did understand why he had been arrested.

The case against him in this country is being prosecuted by Daniel Butler of the Criminal Division’s Fraud Section, on detail from the Special Inspector General for Afghanistan Reconstruction (SIGAR). The case is being investigated by the Defense Criminal Investigative Service, SIGAR, FBI, U.S. Army Criminal Investigation Command, Air Force Office of Special Investigations and Internal Revenue Service-Criminal Investigation.