Hospitals and nursing homes are among the late adopters, in part because of the complexity of rolling out technical systems in big institutions. Several of New York’s major health systems are applying for waivers to get more time for at least some of their facilities, including Montefiore Health System, NYU Langone Medical Center, Northwell Health and the Mount Sinai Health System.

Officials say that transmitting prescriptions to pharmacies will cut down on fraud, because people will no longer be able to modify a prescription by, for example, increasing the number of pain pills ordered.

“Paper prescriptions had become a form of criminal currency that could be traded even more easily than the drugs themselves,” said Eric T. Schneiderman, the state’s attorney general, who helped write the legislation. “By moving to a system of e-prescribing, we can curb the incidence of these criminal acts and also reduce errors resulting from misinterpretation of handwriting on good-faith prescriptions.”

Yet electronic prescribing will present its own set of challenges as patients and doctors get used to the idea.

Patients will have to come in knowing what pharmacy they want to use. At Lenox Hill, nurses will ask all incoming patients to indicate a preferred pharmacy, or have them pick one from a list presented by the software.

And if the medication at the pharmacy is either too expensive or not available, there will be no quick fix. To have a prescription sent to another pharmacy, the doctor will have to cancel it by phone and then prescribe it again.

The hospitals acknowledge the difficulties. When trying to convince doctors of the benefits of electronic prescriptions, “I don’t pitch it as, ‘It’s going to be faster for you,’” said Dr. Michael Oppenheim, the chief medical information officer for Northwell Health. Instead, Dr. Oppenheim said, he mentions things like improved legibility and better coordination of care.