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District officials want Jeff Thompson, the alleged shadow financier behind what federal prosecutors say was an illegal effort to get Mayor Vince Gray elected, to pay up to $3.8 million to the Medicaid managed care organization he owns that is currently under city control.

A newly released audit of Chartered Health Plan, the Thompson-owned Medicaid MCO that the city took control of last year because of its shaky finances, found that Thompson owes the company $2.8 million in federal income tax refunds. Auditors also say that there isn’t sufficient documentation to support $1 million that Chartered paid to a Thompson-owned health clinic, Chartered Family Health Center. The city is asking Thompson to either provide records justifying those payments or to reimburse Chartered the $1 million.

This is not the first time that payments from the Thompson-owned Chartered to the Thompson-owned Chartered Family Health Center have been questioned. Thompson settled with the District in 2008 after the city alleged in a civil lawsuit that the health center had overbilled by nearly $4 million. An audit of Chartered Health Plan’s 2005 books found that Thompson’s clinic was charging Chartered more than double the highest rates paid to other clinics for the same services.

In 2004, Thompson refunded the city $2 million after the health center failed to fulfill its contract and keep the center open 24/7, the Washington Times reported.

A. Scott Bolden, who is representing Thompson on Chartered-related matters, had no comment on the audit. City officials are having a teleconference about Chartered and the money they say Thompson owes shortly. LL will update as needed.

Update: Yikes, more bad news for Thompson. The audit also revealed that in order to pay the 2008 settlement with the city, Thompson (or, technically, D.C. Healthcare Systems, Chartered’s Thompson-owned parent company) and Chartered took out a $14 million loan from Cardinal Bank. Only interest payments on the loan have been been made so far, but payments on the principal came due last November. If Thompson defaults, Cardinal can cash in the $14 million worth of Chartered’s assets the bank is currently holding. Thompson would be legally bound to pay Chartered back, but the big question is whether he’d be able to.

Screengrab courtesy of Charles Parsons