"Either Justice officials were not aware of this dilemma, which is hard to believe, or they didn't want to enter into that fray," Djinis said.
A Justice Department spokesman did not respond to a request for comment. FinCEN spokesman Steve Hudak said only that the agency was "reviewing the latest developments."
The Justice Department memo reiterated its commitment to enforcing federal restrictions on marijuana. But it told prosecutors to focus on areas of federal interest, such as distribution to minors, involvement of organized crime, trafficking across state lines and growing on public land. In other cases, enforcement would be a state matter.
Vulnerable to prosecution
Banks handling money from state-authorized marijuana dispensaries may face a money-laundering prosecution by either the federal government or by another state if the funds cross state lines, said Gurule, who is now a professor at the University of Notre Dame law school.
Shunned by banks, dispensaries have flocked to money-services businesses to obtain money orders. But that industry is not well prepared to manage the legal obligations, Djinis said.
"This new policy (by the Justice Department) doesn't solve the problem at all for the financial services community," he said. "If anything, it makes it more cumbersome, more confusing and less satisfying."
For instance, he said, dispensaries that distribute to minors will still face prosecution. But a financial institution would have no way of knowing whether a client had engaged in that or another activity still targeted by federal enforcers.
The medical marijuana business was worth $1.7 billion in 2011 and is growing, according to a study by financial analysis firm See Change Strategy.
Roughly 20 states and the District of Columbia have legalized medical marijuana. Voters in Colorado and Washington state went a step further in November by legalizing recreational use.
But the U.S. Drug Enforcement Administration and the Justice Department probably "will continue to maintain that the proceeds are still illicit," said a former Justice Department official who requested anonymity.
(Read more: Marijuana scams growing like weeds, US regulators warn)
"I don't think the big banks will change their present policy and bank these outfits," he said. "It's not worth the risk."
Even if the Justice Department said financial institutions could serve state-authorized marijuana dispensaries, a regulator or a "rogue" U.S. attorney might have a different view and go after a bank, said Rob Rowe, a lawyer with the American Bankers Association's Center for Legal and Regulatory Compliance.
Some association members have said marijuana should remain illegal, he said, while others see "a viable small business opportunity" to offer banking services.
"But until Congress changes the law," Rowe said, "there is not a lot a bank can do."