The Affordable Care Act, known as Obamacare, is at the center of the budget debate that has resulted in a government shutdown. But one of the ironies of the situation is that the program will remain funded. It even reached a major milestone — the launch of the insurance exchanges — on Oct. 1, the same day other areas of government were forced to place employees on furlough.

The shutdown includes all areas of the government not deemed essential, or those for which exceptions apply. Under these exceptions, the ACA, as well as Medicare and Medicaid, are not affected. But other areas of healthcare, particularly those in the public health arena, don’t fall under the same exceptions and were forced into limbo.

Dr. Joel Blass, medical director at the Workmen’s Circle Multicare Center, a subacute, rehabilitation facility for senior patients in Bronx, N.Y., said he assumed there would at least be a delay in Medicare payments until the shutdown ended.

Blass said he feels terrible for the employees who are furloughed, but it was “very heartening” to learn his patients wouldn't experience a delay in social security checks being delivered. And from a physician’s perspective, it was reassuring to learn Medicare and Medicaid reimbursements would still be going through, he said.

Alex Hecht, Steve Weiner and Andy Shin, attorneys with the international healthcare law firm Mintz Levin, wrote a newsletter to their clients in September explaining the mandatory funding for Medicare, Medicaid and Obamacare. But, they wrote, if the shutdown continues long-term, there could be a delay in claims payments and other administrative functions.

The Department of Health and Human Services published a contingency plan on its website before the Oct. 1 deadline detailing which programs would be closed and which ones would remain open if a shutdown were to occur. It said 52 percent of its 78,198 employees would be furloughed.

The department with the largest percentage of furloughed employees is the Agency for Healthcare Research and Quality at 92 percent, followed by the Substance Abuse and Mental Health Services Administration at 90 percent. At 6 percent, Indian Health Services will feel the least impact. It will continue to provide direct clinical services to patients in its IHS clinics.

In its contingency plan, HHS said that grant-making agencies and those that are “employee-intensive” would have the most staff on furlough. Those that have a direct service component will have the least amount of employees on furlough.

The biggest impact will be felt among researchers and scientists. The elderly, Native American and developmentally disabled populations who rely on service programs will also be impacted.

About 73 percent of National Institutes of Health employees, the majority of whom support NIH research programs, are furloughed. Patients currently at the NIH Clinical Center will continue to be cared for, but new patients will not be accepted into the NIH’s clinical research programs during the shutdown. Researchers at the AHRQ will also be unable to process grants and contracts for patient safety and healthcare outcome research projects.

SAMHSA said it would be unable to monitor grants and contracts, including those requiring on-site supervision. It will, however, continue to run programs such as the Disaster Distress Helpline and Suicide Prevention Lifeline.

The Centers for Disease Control and Prevention is operating with a minimal staff. According to the HHS contingency plan, it will be unable to support the annual seasonal influenza program. Vaccines will continue to be delivered, but the agency will not be able to track the spread of influenza or respond to outbreak investigations. It said it also would be unable to update treatment and prevention recommendations for diseases and viruses such as HIV, tuberculosis, sexually transmitted diseases and hepatitis.

Other programs not deemed essential, but that could have potentially dangerous consequences if not in operation, are those administered by the Administration for Community Living. ACL programs placed on hold include senior and Native American nutrition services and support services, prevention of elder abuse and neglect programs, and protection and advocacy programs for persons with development disabilities.

According to the ACL’s 2014 budget, “Nutrition Services help approximately 2.5 million older adults receive the meals they need to stay healthy and decrease their risk of disability.”