The money was virtual, but prosecutors say the crime was real.

Officials brought charges against a group of men who allegedly manufactured an Internet-based currency to launder about $6 billion in ill-gotten gains, a sign of authorities' rising concern with digital cash.

The charges, in an indictment unsealed Tuesday, describe a complex online system set up by a Costa Rica-based organization called Liberty Reserve. The system allegedly was designed to give criminals a way to move money earned from credit-card fraud, online Ponzi schemes, child pornography and other crimes without being detected by law enforcement.

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Liberty Reserve, which was incorporated in 2006, was a "bank of choice for the criminal underworld," according to the indictment, which said the operation allegedly laundered the money through 55 million transactions before it was shut down earlier this month. The company has about one million users world-wide, including about 200,000 people in the U.S., according to prosecutors. They called the plot one of the largest money-laundering operations ever uncovered.

A spokesman for Liberty Reserve couldn't immediately be reached for comment. Prosecutors said Tuesday that they arrested five of the seven men charged in the indictment Friday in Spain, Costa Rica and Brooklyn, N.Y., and charged them with operating an unlicensed money-transmitting business. The officials said they plan to seek extradition of those arrested abroad, and that the two remaining men are at large.

The indictment against Liberty Reserve comes amid a concerted effort by Washington to police the nascent world of virtual currencies and ensure operators comply with U.S. law.

On Tuesday, in the first use of the 2001 Patriot Act against a virtual currency, the Treasury Department invoked a section of the law to choke off Liberty Reserve from the U.S. financial system. The Treasury's proposal would prohibit U.S. financial institutions from opening or maintaining accounts for foreign banks that process transactions for Liberty Reserve and require special steps to guard against any transactions involving it.

Virtual currencies, most notably bitcoin, still account for only a tiny fraction of global transactions, but they are being embraced by some Internet merchants and are used in a host of legitimate transactions—for example, Web services and online-dating sites.

Law-enforcement officials are concerned about criminals' ability to move around money outside the regulated world of banks and traditional money-moving services such as Western Union. Officials recently warned that digital currency exchanges should follow traditional anti-money-laundering rules.

The rise of virtual currencies has been exemplified by bitcoin, which lets Internet users create new money by solving complex math problems. The currency, which launched in 2009 and has gone through some wild spikes in value this spring, has attracted the attention of established companies and venture capitalists alike.

Tuesday's case doesn't involve bitcoin, though the virtual-cash community was watching developments closely.

"I think it is just another giant, flashing warning light to bitcoin exchanges: If you're not compliant, there are some serious risks, both at the federal and state levels," said Patrick Murck, legal counsel for the Bitcoin Foundation, a trade group that promotes bitcoin software and security standards.

Preet Bharara, the Manhattan U.S. attorney, said at a news conference Tuesday that he believed "virtually all" of Liberty Reserve's customers used it for criminal purposes, though he said legitimate users can seek to recover funds.

Mr. Bharara didn't give details on the alleged criminals but said the investigation was continuing. "There's more to come," he said Tuesday, adding that the case has so far involved seizing $25 million dollars in 45 bank accounts around the world.

Prosecutors allege Liberty Reserve facilitated a range of criminal activity by allowing alleged criminals to conduct transactions using its digital currency, "LR." The system is opaque, and Liberty Reserve deliberately kept the users anonymous and untraceable, prosecutors said.

A transaction would start with one person opening a Liberty Reserve account using a false name and address, including what prosecutors said were blatant criminal monikers such as "Russia Hackers" or "Hacker Account."

That person would wire real currency such as dollars to approved third-party currency exchangers in countries including Russia and Nigeria. The exchangers would convert the dollars into LRs and deposit them into the person's Liberty Reserve account.

From there, a criminal could buy narcotics, stolen credit-card numbers or other goods by transferring the LRs to another person's Liberty Reserve account. The recipient of the LRs could go to another unregulated currency exchanger and convert the LRs back into dollars.

Liberty Reserve charged a 1% fee for LR currency transfers and an additional "privacy fee" of 75 cents per transaction to hide Liberty Reserve account numbers, making the transfer virtually untraceable.

Preet Bharara, U.S. Attorney for the Southern District of New York Reuters

Liberty Reserve made an appearance in a criminal case earlier this month. Federal prosecutors in Brooklyn, N.Y., accused eight people of stealing about $45 million from automated-teller machines throughout New York City using stolen prepaid debit-card numbers. Prosecutors said at least one of the men used an account at the online-currency operator to transfer some of the allegedly stolen funds.

James T. Hayes Jr., special agent-in-charge of the New York field office of the U.S. Immigration and Customs Enforcement's Homeland Security Investigations, said his agency became aware of possible wrongdoing at Liberty Reserve in 2010 and teamed up with the Internal Revenue Service to investigate the matter.

The indictment described how two of Liberty's founders, Arthur Budovsky and Vladimir Kats, were convicted in 2006 in New York for operating Gold Age Inc. as an unlicensed money-transmitting business.

Lawyers for Mr. Budovsky and the other defendants named in the indictment couldn't immediately be reached for comment. A lawyer for Mr. Kats declined to comment.

The indictment said Liberty Reserve also caught the attention of Costa Rican regulators in 2009, forcing the company to allegedly set up a fake compliance system. In late 2011, the Treasury Department warned financial institutions about the risks of doing business with Liberty Reserve.

In an Internet chat-room exchange included in the indictment, one defendant allegedly said he knew the company's activities were "illegal" and said "everyone," including the U.S. Department of Justice, knows Liberty Reserve "is a money-laundering operation that hackers use."

About two weeks after the Treasury's warning note, Liberty Reserve "went underground," the indictment says, and continued to operate in Costa Rica using a "stripped-down staff working out of an office space held in the name of shell companies." The defendants also allegedly tried soon after to drain their bank accounts.

Write to Reed Albergotti at reed.albergotti@wsj.com and Jeffrey Sparshott at jeffrey.sparshott@dowjones.com