Food and Drug Administration Commissioner Margaret Hamburg steps down from her post this week as the agency grapples with an one of the most contentious issues of her tenure: how to regulate electronic cigarettes.

Hamburg is recognized for her efforts to rein in tobacco companies over the last six years, but observers of a battle that’s pitting a burgeoning industry against public health advocates say her legacy is still being shaped.

Hamburg, 59, is retiring just months before the agency is expected to issue sweeping new e-cigarette regulations.

Public health groups say they hope her departure won’t affect the outcome of the rules.

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“She has been a great champion in the fight against tobacco,” said Gregg Haifley, director of federal relations at the American Cancer Society Cancer Action Network. “You don’t save lives by reducing the number of cigarettes people smoke, but by reducing the number of people who smoke.”

Hamburg helped shape the e-cigarette rules as one of her last acts as FDA commissioner, public health advocates say.

Taking the helm of the FDA in the first months of the Obama administration, Hamburg told The Hill that she hopes the regulations will stand as part of her record.

“I would love to see the rule get done,” she said.

But the FDA is finding it difficult to find a middle ground on the e-cigarette regulations.

While the health groups say they are disappointed that the e-cigarette regulations aren’t stronger, industry groups claim they have been unfairly targeted by the FDA under Hamburg — and hope her successor will be more lenient in the upcoming regulations.

The FDA’s rules, as proposed, could completely “wipe out” the e-cigarette industry, said Julie Woessner, president of the Consumer Advocates for Smoke-free Alternatives Association.

The FDA originally floated the idea of regulating e-cigarettes back in 2011, but four years later, public health advocates say they’re still waiting.

The regulations were formally proposed last year to much criticism from both public health and industry groups. The final rule is expected in June.

Hamburg’s departure is “not an excuse” for even more delay, public health advocates say.

“Every bit of delay is a new opportunity for the tobacco industry to hook new people on nicotine and get in the way of helping tobacco users quit,” Haifley said.

The so-called deeming rule would give the FDA authority to regulate modern-day smoking devices like e-cigarettes that are currently out the agency’s control.

But completing the deeming rule is only the first step toward regulating e-cigarettes.

Once the FDA asserts its power, the agency would then need to issue subsequent e-cigarette regulations to address a number of different issues, such as age and marketing restrictions. The process could take years to complete, experts say.

Public health advocates are also pressing for restrictions on online sales, as well as the flavoring and advertising used by e-cigarette companies.

E-cigarettes that are marketed with candy and fruit flavors subtly target young smokers, public health advocates warn. They also say it’s difficult to verify a customer’s age over the Internet.

However, says Gregory Conley, president of the American Vaping Association, e-cigarettes do more good than bad for public health.

Conley argues the innovative smoking devices can help ween adult smokers off traditional cigarettes, which he says are more harmful than e-cigarettes.

Hamburg, he said, will ultimately find herself on the wrong side of history.

“When people look back in 100 years, they’re going to see e-cigarettes helped thousands of people quite smoking,” Conley said. “But fighting against e-cigarettes is the legacy she will leave behind.”

This story updated at 11:04 a.m. to correct Haifley's organization. He works for the American Cancer Society Cancer Action Network.