Some federal programs are not funded through the yearly appropriations process. This includes programs such as Medicare and Social Security benefits which are “mandatory programs” and affected by the appropriations process. While these benefits will continue during the shutdown, there may be fewer people to administer them because the staffing at these agencies is paid for through yearly appropriations.
Other programs, including many at the Food and Drug Administration are funded through user fees, and some, like the Veteran’s Administration, can use advanced appropriations for funding, so their operations continue.
Programs that are funded through the annual appropriations process may continue to operate on a limited basis. Programs or projects deemed “essential,” such as those focused on security, safety, human health, or other projects deemed “mission critical,” will continue to operate. However, the federal employees that run these programs will not be paid until the federal government is funded.