Health Secretary Robert F. Kennedy Jr. has maintained strict public silence on vaccines in recent months, exactly as ordered by a White House concerned that his views could damage Republicans in November’s midterm elections. Instead, he has redirected that energy into a sprawling, top-priority research operation across every agency under his control.

According to six people familiar with the effort, who spoke on condition of anonymity because they were not supposed to discuss it, Mr. Kennedy has instructed government scientists and data contractors to treat his belief that vaccines are driving an epidemic of chronic disease as an urgent national security matter. The inquiry, led by Martin Kulldorff, the department’s new chief science and data officer, is re-examining whether vaccines cause autism, whether thimerosal remains dangerous in flu shots, and whether the entire schedule is responsible for rising rates of asthma and autoimmune disorders.

“We were told he can’t go on podcasts yelling about it anymore,” said one FDA researcher. “So now we just quietly spend every workday trying to prove it with millions of patient records. Same difference.”

Career scientists at the CDC and FDA have been pulled into the project alongside outside contractors granted access to vast medical databases. One participant described the standing order as “find the link, preferably before November, but don’t tell anyone we’re looking.”

A White House official expressed satisfaction with the arrangement. “Bob has shown admirable restraint by keeping all his strongest opinions inside classified research channels where voters will never hear them.”

At press time, sources confirmed the study’s timeline had been quietly moved up to ensure any supportive findings can be released the day after polls close.