Prospective pot shop owners be warned: New England’s top narcotics cop says federal agents won’t hesitate to come down on dispensaries that pop up next year under the Bay State’s medical marijuana law.

John J. Arvanitis, special agent in charge of the Drug Enforcement Administration’s New England Division, told the Herald in an exclusive interview that the feds will probe pot pharmacies as they see fit.

“Marijuana is still a controlled substance,” Arvanitis said. “DEA is committed to investigating individuals who are involved in the distribution of marijuana. DEA goes to where the information and evidence take it. If we become aware that individuals are involved in marijuana distribution, we’ll investigate it.”

Arvanitis’ comments during a wide-ranging interview about his new position reflect the official position of the DEA, which has long opposed medical marijuana and has worked to shut down hundreds of dispensaries out West.

His tough talk comes as Massachusetts rolls out a new law allowing doctors to prescribe pot for patients with cancer, AIDS, Parkinson’s disease and other illnesses. Up to 35 pot shops, regulated by state health officials, will open in 2013.

But making the law work won’t be easy.

California’s 1996 law is criticized as vague even by pro-pot activists, who say federal prosecution has been “chaotic, unpredictable and capricious.”

“We need clear direction from the Department of Justice, and the Obama administration has utterly failed to give that,” said Dale Gieringer, director of California’s division of the National Organization for the Reform of Marijuana Laws.

Federal authorities have been on a prescription pot crackdown for the better part of a year, shutting down large dispensaries and threatening to shutter others, saying they were raking in big bucks and serving as fronts for drug runners. In September, for example, prosecutors in Los Angeles sued to seize the assets of three shops and sent warning letters to 68 others, essentially ordering them to close by giving them two weeks to comply with federal law.

In Colorado, authorities in 2010 raided a Denver-area medical marijuana provider who showed off his grow operation on a local TV newscast. He is serving a five-year sentence in federal prison in Leavenworth, Kan.

In Maine, the feds have so far stayed away from the eight state-licensed dispensaries allowed under a 2009 prescription pot law.

“It’s certainly always something we’re aware of,” said Becky DeKeuster, executive director of the Wellness Connection of Maine, which runs four dispensaries. Arvanitis’ comment, she said, “puts us all in an interesting position.”

Arvanitis’ warning didn’t seem to worry John Napoli, who is hoping to open a dispensary at his downtown hydroponics shop, Boston Gardener.

“Before it was banned in the 1930s, cannabis was available at every pharmacy in Massachusetts,” he said. “I think we’re headed back in that direction. The DEA will eventually follow the people’s lead.”