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The sale of nearly all marijuana vapes will remain prohibited in Massachusetts, after the Cannabis Control Commission on Tuesday ordered licensed shops and dispensaries to quarantine the products.

The decision is the latest repercussion from Governor Charlie Baker’s nearly two-month-old ban on vape sales. His move, in response to a spate of vaping-related lung illnesses that has sickened more than 2,000 Americans and killed at least 40, has drawn sharp pushback but remains in effect for the general public.

Under a recent court ruling, the independent commission had faced a noon deadline Tuesday to either lift the part of the ban affecting marijuana vape sales — though only for medical marijuana patients — or keep it in place.

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The commission’s executive director, Shawn Collins, said in an order sent to licensed marijuana companies that regulators are still investigating whether oil vapes made by regulated operators are safe, and temporarily quarantined those products. The commission said the quarantine was based on Collins’s “determination that these products pose an immediate or serious threat to the public health, safety, or welfare.”

However, Collins declined to uphold Baker’s ban on the purchase of flower vaporizers, a separate category of device, by medical marijuana users. Other consumers are still barred from buying any type of vape, including flower vaporizers.

Will Luzier, a cannabis advocate and medical marijuana patient who has sued over the ban, called the decision “unfortunate” and said the commission should quickly test vapes and clear them for sale.

“The quarantine and testing of all these products probably could’ve taken place months ago,” Luzier said. “It’s unfortunately very late in the game to take that action.”

A spokesman for Baker said the governor’s administration “appreciates the commission’s careful consideration of this important patient safety issue and supports the move to quarantine these products.”

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Baker has previously said that the unusually broad ban — the strictest in the country — is necessary because the exact cause of the lung illnesses remains unclear. Federal health officials have said most of the illnesses probably were caused by vitamin E acetate and other additives in illicit marijuana vape cartridges.

The commission noted Tuesday that a study by officials in Wisconsin and Illinois had concluded that the vast majority of illnesses were linked to vapes obtained from “informal” sources — but also said regulators had yet to definitively determine whether any regulated vapes made by licensed Massachusetts companies contained vitamin E acetate.

MCR Labs, a licensed cannabis testing laboratory in Framingham, has said it had found vitamin E acetate in nine of 109 marijuana vape cartridges it has tested on behalf of consumers and companies since late September. The nine contaminated cartridges all came from unlicensed sources, MCR said.

Baker’s ban has drawn legal challenges from nicotine vape manufacturers and retailers, plus medical marijuana patients who said they relied on vapes to treat severe pain and other chronic conditions.

Last month, Suffolk Superior Judge Douglas H. Wilkins ruled that Baker’s administration had unconstitutionally exceeded its authority by imposing the ban unilaterally and without holding public hearings — but allowed it to remain in place while officials took steps to formalize the policy as an emergency regulation.

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In another ruling last week, on a request to lift the ban on vape purchases by registered medical marijuana patients, Wilkins said health officials in Baker’s administration had trampled on the commission’s exclusive legal authority over cannabis products. He gave the commission a week to either uphold the ban or let it expire, though the ruling only applied to purchases by medical marijuana patients, not recreational consumers. The agency’s five commissioners declined to endorse the ban, and instead kicked the decision to Collins.

Up until the moment Collins imposed the quarantine, many medical marijuana patients had held out hope they would be able to purchase vapes Tuesday.

Registered patient Frank Shaw, 66, of Ipswich went to the New England Treatment Access dispensary in Brookline on Tuesday morning hoping to stock up. Shaw, one of four medical marijuana patients who sued the state over the ban, said oil vapes are the most effective treatment for his severe chronic foot pain that stems from nerve damage.

Patients “can’t get their medication that they need for their medical condition,” Shaw said. “It’s devastating.”

At a Tuesday press conference organized by opponents of the ban, cannabis commissioner Shaleen Title said the quarantine was based on “credible evidence.” She cited the CDC’s recent finding regarding vitamin E acetate and the commission’s ongoing efforts to verify that the chemical was not present in regulated vapes. But she also insisted the quarantine was not “an open-ended ban.”

“I feel obligated to speak out about perhaps the most ill-considered policy that I’ve seen implemented in my whole time in public office,” Title said of Baker’s ban. “It’s cruel, it’s inhumane, and it’s ineffective.”

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Noting that most illnesses have been linked to illicit market products, Title added that the ban was “sending patients and consumers to the source of that danger.”

It is not clear where and how medical marijuana patients might now purchase flower vapes, battery-powered devices that heat ground-up marijuana flower — industry terminology for the plant’s buds — in a small oven without combusting it. Flower vapes have not been publicly linked to any of the cases of vaping-relating lung illness and are sold without any marijuana included. Before the ban, they were widely available in vape stores and head shops, and less commonly at licensed marijuana shops.


Dan Adams can be reached at daniel.adams@globe.com. Naomi Martin can be reached at naomi.martin@globe.com.