FBI spokesman Richard Kolko said that FBI agents, acting at the request of the SEC (Securities and Exchange Commission), had served the papers on Sir Allen in Fredericksburg, Virginia.
The Texan cricket impresario is accused of luring investors with promises of improbable and unsubstantiated high returns on certificates of deposit and other investments.
The SEC needed to serve the papers to ensure that he turned in his passport and was made aware of the proceedings against him, the BBC's Richard Lister reports from Washington.
Stressing that Sir Allen had not been arrested, Mr Kolko said he did not know if he had actually surrendered his passport.
Giving few details, he said that agents from the FBI's office in Richmond, Virginia, had "located and identified Stanford Financial Group chairman Allen Stanford in the Fredericksburg, Virginia area".
The papers were served about 1345 local time (1845 GMT) on Thursday as Sir Allen sat in a car, and the authorities do not believe he had been purposely hiding from them, an unnamed law enforcement source told the Associated Press.
ABC News quoted one of the billionaire's lobbyists, Ben Barnes, as saying that Sir Allen had been "very depressed".
STANFORD'S FINANCIAL EMPIRE
The first Stanford company was founded in Texas in 1932 by Lodis B Stanford, Sir Allen Stanford's grandfather
Stanford Financial Group is a complex worldwide network of affiliated financial services companies
The group reports it has over $50 billion in assets
Stanford International Bank is an Antigua-based affiliate with $8.5bn in assets and 30,000 clients around the world. Sir Allen Stanford is a chairman and sole shareholder
Sources: Corporate websites, Securities and Exchange Commission
He had sought to end a federal manhunt for him by directly approaching officials at the US justice department, Mr Barnes added.
Sir Allen's father, James Stanford, told AP in Mexia, Texas, that he hoped the allegations against his son were untrue.
"I have no earthly knowledge of it," said the 81-year-old, listed as chairman emeritus and a director for Stanford Financial Group.
"I would be totally surprised if there would be truth to it. And disappointed, heartbroken."
Asked what advice he would give his son, he said: "Do the right thing."
Earlier, Peru and Venezuela became the latest countries to intervene in local banks controlled by the Stanford group.
Stanford father believes in son
Peru's securities regulator suspended local operations of the Stanford Financial Group for 30 days and Venezuela said it would take control of Stanford Bank Venezuela.
Panama, Ecuador and Antigua also took action after the accusations against Sir Allen were reported.
Regulators were hoping to calm customers worried about investments as queues of worried investors have formed at banks associated with him in the US, the Caribbean and Latin America.
A civil court judge in the US has frozen the assets of Sir Allen and those of the Stanford Group, its Antigua-based subsidiary Stanford International Bank (SIB), and another subsidiary, investment adviser Stanford Capital Management.
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