Sir Allen denies any wrongdoing and has not been charged
Charges have been brought against Laura Pendergest-Holt, chief investment officer at the Stanford Financial Group of US tycoon Allen Stanford.
She is charged with conspiring to obstruct a Securities and Exchange Commission (SEC) investigation into the firm, and obstructing the inquiry.
Each count carries up to five years in jail and a fine of $250,000 (£165,000).
Sir Allen is accused of fraud worth 8bn (£6bn) but has not been charged and denies wrongdoing.
Ms Pendergast-Holt's lawyers did not comment on the development.
The SEC, the US financial watchdog, has described the alleged fraud at Stanford Financial group as a "fraud of shocking magnitude".
The cricket impresario is accused of luring investors with promises of improbable and unsubstantiated high returns on certificates of deposit and other investments.
The billionaire financer has refused to talk to US regulators investigating his alleged fraud, with court documents having shown that Sir Allen pleaded the Fifth Amendment - the right to withhold potentially self-incriminating evidence.
In an interview with ABC last month he insisted no money was lost by customers dealing with his financial services companies.