FORTUNE — Acceptance of medical marijuana, and the patients who medicate with marijuana, is sweeping state legislatures across the country. Of the 21 states that have passed laws addressing medical marijuana, nine have done so in the past three years. A growing number of Americans appear willing to allow those with chronic illness or pain to alleviate their symptoms with the plant, quite apart from the issue of recreational use, which Colorado and Washington state recently approved.

But even as recreational usage is gaining acceptance, people who medicate with marijuana across most states can still get fired for failing their employers’ drug test. Both Washington and Colorado have legalized recreational marijuana use, but it’s still unclear whether employees’ jobs are protected in those states if they smoke off duty — either for recreation or medical use. In Colorado, for instance, the marijuana law allows employers to impose any drug policies they see fit.

There are a lot of unanswered questions, and it’s time for U.S. lawmakers to clarify how companies should treat these cases. Regardless of a state’s law, using marijuana remains a violation of federal law. This conflict has important consequences in the workplace: Employees are left with no protection and employers with little guidance.

MORE: 3 ways to reignite U.S. job creation 

Moreover, in a 2013 ruling, the Colorado Appellate Court said that because marijuana is still illegal under federal law employees could be fired for using it off duty.The case has gone to the Colorado Supreme Court; if it rules in favor of the employee, it would provide protection to thousands of medical marijuana users in Colorado and potentially influence other states to follow. If the court decides in favor of the employer, the status of registered users in Colorado remains unchanged: They have very little protection from losing their job.

Take the case of former Wal-Mart WMT employee Joseph Casias, who medicated with marijuana, off duty, in accordance with Michigan’s Medical Marijuana Act to alleviate the symptoms of his sinus cancer and brain tumor. In 2009, after a workplace injury, he failed a company drug test. Wal-Mart fired him. The Michigan court upheld his firing because the state’s medical marijuana law did not regulate private employment; it merely provided a defense against criminal prosecution. Similar incidents have occurred in California, Washington, and Oregon. Courts there have ruled in favor of employers who fired people for testing positive for marijuana though they were medicating with it off duty and in accordance with state laws.

MORE: The Nazis stole my art

A few states have anticipated this conflict, but only two provide real protection for employees like Casias. Arizona and Delaware specifically prohibit employers from terminating registered medical marijuana users if they test positive for marijuana, provided it is not being used at the workplace.

Three states provide limited protection for a person’s status as a registered user or registered primary caregiver, but they offer no protection if that registered user tests positive for marijuana.

For example, Rhode Island employers (and schools and landlords) cannot refuse to employ someone just because he or she is a registered user or a registered primary caregiver. In Maine and Connecticut, patients cannot be discriminated against at work simply because they are registered users.

But where does that leave someone like Brittany Thomas in Maine? Thomas, 24, suffers from severe back pain and was taking prescription narcotics to control it. After consulting with her doctor, she switched to marijuana because it controlled her pain without the debilitating side effects of prescription painkillers. When her employers told her she would have to complete a drug test, she informed them that she would not pass because she was a registered medical marijuana user. She failed the test and was terminated. Her lawyer identified the problem medical marijuana users face: “No patient should be forced to choose between the pain relief she needs to live a normal life, and the employment she needs to support her family.”

MORE: Who are the entrepreneurs?

The irony is painfully obvious. Many medical marijuana users like Thomas would likely keep their jobs if only they used the much more powerful prescription drugs. Is this the result voters anticipated when they voted to support medical marijuana? A lawyer who represented a woman in a case similar to Thomas’ thinks that “it would flabbergast the average voter to think, ‘I’ve been given this right but can get fired for it anyway.’” And it’s an irony that undermines the market that would supply sufferers with an alternative to traditional medications. How can this market get off the ground if customers could lose their jobs for using the product?

Medical marijuana isn’t going away; its acceptance is only gaining momentum. However, its support is only meaningful if users don’t lose their jobs.

Kabrina Krebel Chang is assistant professor of business law and ethics lead of the Undergraduate Program at Boston University School of Management.