Federal officers Monday charged an in-house compliance officer and another executive of a Bitcoin exchange company with money laundering and other felonies. It is believed to be the first time a company’s compliance officer has been charged with a crime related to Bitcoin, the Internet-based alternative currency.

Charged [PDF] was Charles Shrem IV of New York, who served as a chief executive and compliance officer at BitInstant. Shrem, who apparently is not a lawyer, was arrested yesterday at John F. Kennedy airport in New York and couldn’t be reached for comment.

Shrem is also listed as vice chairman of the Bitcoin Foundation, and owns the EVR bar in New York, which accepts Bitcoin for payment. Patrick Murck, general counsel of the foundation, did not immediately return messages.

Also charged was Robert Faiella, a Bitcoin exchanger based in Florida.

The federal complaint [PDF] accuses the two men of laundering money related to drug proceeds from users of the now-defunct website Silk Road. The site sold drugs and other illicit products to people who paid with Bitcoin, a virtual nongovernment currency that cannot be traced.

Agent James Hunt of the Drug Enforcement Administration said in a statement, “Drug law enforcement’s job is to investigate and identify those who abet the illicit drug trade at all levels of production and distribution including those lining their own pockets by feigning ignorance of any wrongdoing and turning a blind eye.”

He accused the defendants of “hiding behind their computers” while breaking the law and helping others break it.

The complaint accuses Shrem of conspiring with Faiella to sell over $1 million in Bitcoins after knowing that the coins would be used to buy illegal drugs on the website.

Each defendant is charged with conspiring to commit money laundering, and operating an unlicensed money transmitting business. Shrem is also charged with failing to file a suspicious activity report regarding the illegal transactions, in violation of the Bank Secrecy Act.

The feds said Shrem “was in charge of ensuring the company’s compliance with federal and other anti–money laundering laws.” The company, which was registered with the U.S. Department of the Treasury, went out of business last July.

The complaint includes email exchanges between Shrem and Faiella that show that Shrem clearly knew what the Bitcoins were to be used for. Other emails have Shrem advising Faiella on how to get around banking policies and anti–money laundering restrictions.

In one such exchange, according to the complaint, Faiella asked how a customer could deposit $5,000 to buy Bitcoins without raising any red flags. Federal law requires the bank to verify the identity—including the tax identification number—of any customer placing an order or series of orders over $3,000.

Shrem replied: “If I were you, I’d spread it out over 2–3 branches to play it safe. … Feel me?”