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 the other accused as well as those of the Stanford Group, its Antigua-based subsidiary Stanford International Bank (SIB), and another subsidiary, investment adviser Stanford Capital Management.
Peruvian regulators acted after queues of anxious customers gathered at a branch in Lima.
In Venezuela, Finance Minister Ali Rodriguez said the government would take control of Stanford Bank Venezuela, after a wave of panic withdrawals, even though the bank's assets are separate from SIB.
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, 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 said that the job of the Venezuelan government was to make sure that what he called "the capitalist crisis" did not affect the Venezuelan economy.
Mr Rodriguez said the government would be looking for an explanation from the US authorities about the charges and the financial health of SIB.
The Venezuelan government assured investors that the economy was stable and denied that the decision to intervene in the bank was indicative of wider financial problems.
A local arm of Stanford Financial Group also halted its activities on the stock exchange in Colombia on Wednesday, and Mexico was also said to be considering measures.
The BBC's Greg Wood, in Houston, said a steady flow of people had turned up at the Stanford group's headquarters in the city on Wednesday, trying find out what had happened to their money.
Hundreds of depositors of Sir Allen's Bank of Antigua in Antigua also sought to withdraw their funds on Wednesday, although the bank is separate from SIB.
The SEC said no-one but Sir Allen and James Davis, SIB's chief financial officer, knew where most of cash has been invested and accused both men of failing to co-operate with investigators.
Filing a case in the civil courts against Sir Allen, the SEC described the case as "fraud of shocking magnitude that has spread its tentacles throughout the world".
John Fuller, an Antigua-based criminal attorney who has known Sir Allen for 10 years, said the financier would be likely fight hard against the charges.
"He's run a very clean - when I say clean, I mean shiny operation. But one does not know what is going on behind the scenes.
"He could be anywhere. This is a man who has means at his fingertips. He's not a man who's going to take any of this lying down. He will fight it. He will mount a campaign to show that he is a victim rather than the perpetrator. He is a fighter."
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