Gov. Andrew Cuomo signed the measure into law on Saturday and held a formal signing ceremony on Monday to highlight the new law.
When the program gets up and running in about 18 months, patients with diseases including AIDS, cancer and epilepsy will be able to obtain non-smokeable versions of the drug.
Instead, the drug must be ingested or administered through a vaporizer or oil base.
Cuomo, a Democrat, says prohibiting smokeable marijuana will help keep the drug out of the wrong hands.
The compromise was one of the final measures passed by lawmakers before they adjourned last month.
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