After nearly two months of red tape and emergency pill supplies, confusion over prescription medication coverage caused by a massive overhaul of national prescription drug coverage has finally begun to draw to a close for some New Haven residents.

The national prescription medication coverage under Medicare was expanded beginning Jan. 1, but this move created a complex network of insurance carriers and left many pharmacies scrambling to fill their patients’ orders while trying to make sure they would get reimbursed. The national plan affected 21 million people, including nearly 3,000 covered by the Yale Health Plan who switched over to the new coverage this year, according to Catherine Sharafanowich, the pharmacy director at New Haven’s Hill Health Center medical clinic.

Hill Health Center found itself in the same position as many other pharmacies across the country, inundated with customers and finding little or no help navigating the complexities of the program change. Sharafanowich said the frustrations came when staff were unable to help patients because the help desks at insurance companies were unavailable to figure out how to enroll eligible patients under Medicare D, part of the new federal prescription drug program.

“We couldn’t get accurate information,” she said. “It was awful, but it’s over.”

Though patients at Yale University Health Services have had an easier transition because the private plan Yale sponsors has more comprehensive coverage than the new Medicare D plan, YUHS has still been inundated with mailings, said Margaret Hionis, Medicare and retiree coordinator at UHS Member Services. Only 50 of the nearly 3,000 patients on the Yale plan who were eligible for coverage applied to switch plans. The implications of such a change were unclear at the time, and many patients who chose to switch did not realize they were better off keeping the Yale plan, said Charles Paul, director of human resources technology and decision support.

“The advice for most Yale retirees is to remain in Yale’s plan so they don’t have to do anything,” he said. “Yale retirees are fortunately insulated from much of the confusion because we maintain a plan that is creditable [under Medicare].”

Now that the help lines are accessible, Sharafanowich said, patients at Hill Health are being enrolled in plans that best cover the prescriptions they need. Although the temporary transitional coverage measures are still in effect, the backlog of enrollment and confusion over plan changes that lead Hill Health to give out limited supplies of prescriptions for free has now been resolved, she said.

“We’re still helping people sort through what plan might be best for their prescription,” Sharafanowich said. “I would say it’s working reasonably well.”

Patients under UHS’s current prescription policy will see a decrease in the cost of their plan when Yale begins to receive compensation from the federal government for those patients who are Medicare-eligible, Paul said. Although the patients themselves will see little of the change, he said, the Medicare program will prevent a large increase in the cost of prescription drugs due to inflation of health care expenses.

“A new cottage industry has grown up around this,” Paul said. “It’s a task, but for a 28 percent subsidy it’s worth it. … Should the law have been simpler? Absolutely. But for an institution that already has a plan in place, it’s not as bad as the people who are out there on their own.”

May 15 is the last day to enroll in a Medicare D plan for this period. The next opportunity to enroll will be Dec. 31.