Hookah bars in the city have a little something extra in the sweet-smelling shisha their patrons enjoy, according to a city Health Department investigation announced yesterday.

While shisha is a sticky combination of herbs, fruit base, molasses and tobacco smoked through a water pipe, the city's 2002 smoking ban forced hookah bars to sell a tobacco-free version. But city health officials said they found that shisha taken from 13 hookah bars in Manhattan and Queens all contained tobacco.

"These 13 hookah bars are knowingly flouting the law by serving tobacco-based shisha," Health Commissioner Dr. Mary Bassett said in a statement.

The city Health Department will start the process of stripping the hookah bars of their permits, according to the agency.

This is the first undercover invesitgation by health officials into hookah bars' compliance with the smoking ban, according to the agency. Of the 2,700 violations issued last year for breaking the smoking ban, 373 of them were issued for use of tobacco in a food service establishment, according to the Health Department.

Mustafa Ali, manager of Sahara East, one of the 13 hookah bars, criticized the city's clandestine investigation, denying that there is any tobacco in the shisha he sells. Ali said his shisha from India was last tested about five years ago and it passed muster then.

"We use zero nicotine tobacco," Ali said. "It's a dry fruit, all of it."

He said he would put up a fight against the Health Department's attempt to revoke Sahara East's permit.

"It's a sad story, just to shut business down," Ali said.

Health inspectors in November teamed up with NYU students to take samples from the 13 bars, chosen for being popular and located close to college campuses like Columbia and NYU, as well as for past violations, according to Thomas Merrill, general counsel for the Health Department. Arista Laboratories handled the testing.

"I would suspect that if you went into the vast majority of hookah places it's going to be tobacco," Merrill said. "I'm not surprised these are the results we got."

Hookah bars are also popular with the young adult and teen set, raising concerns that 18-year-olds are buying tobacco; in 2013, the city raised the age for buying tobacco to 21.

"That's why we included the NYU students," Merrill said.

There were six NYU students majoring in public health who teamed up with Health Department investigators for the Nov. 14 recon mission for shisha samples. Their professor, Diana Silver, recruited and trained them for a crash course in how public health laws work in real life.

"There's a real issue here and whatever it is that hookah bars are actually selling, they need to ensure the content doesn't have nicotine in it," Silver said.