There are currently 1,001 measles cases according to the agency, 20 more cases than the Centers for Disease Control and Prevention (CDC) reported Monday in its weekly update.
Health and Human Services Secretary Alex Azar said in a statement that the agency is "promoting the safety and effectiveness of vaccines amid concerning signs that there are pockets of undervaccination around the country".
"The 1,000th case of a preventable disease like measles is a troubling reminder of how important that work is to the public health of the nation," Azar said.
"We cannot say this enough: Vaccines are a safe and highly effective public health tool that can prevent this disease and end the current outbreak.”
This year's record number of cases has been largely fueled by hotbeds in New York City and Rockland County, New York, where cases have continued for seven months among ultra-Orthodox Jewish communities which typically do not vaccinate their children.
Measles was officially eliminated in the U.S. in 2000, a milestone officials define by the virus no longer circulating continuously.
The CDC warned that if outbreaks continue through the summer and fall, the U.S. risks losing its measles elimination status, noting should that happen, "that loss would be a huge blow for the nation and erase the hard work done by all levels of public health".
It said in the decade before 1963 when a vaccine became available, roughly 3-4 million people contracted the virus annually in the U.S., resulting in between 400 to 500 deaths each year and 48,000 hospitalizations.
The CDC has been implementing a number of initiatives to combat the spread of the disease, including deploying a field team to Rockland County to help diagnose cases, identifying 1,500 people who were exposed to measles while traveling. It has also deployed an immunization worker to Albany, New York.
The number of measles cases this year is the highest since 1992, when 2,237 cases of the disease were reported in the U.S.