“There are scientists who work for this government who do not want America to get well, not until after Joe Biden is president,” he told his 5,000 followers.
Mr Caputo, 58, is a longtime friend of the US president and was appointed to his post in April, despite having no background in healthcare.
In his role, he co-ordinates messaging for the US Department of Health, which is at the center of the US coronavirus response and oversees the CDC as well as the Food and Drug Administration and the National Institutes of Health.
In his Facebook Live video, Mr Caputo also warned that left-wing hit squads would lead an armed opposition if Mr Trump won the election, saying: “If you carry guns, buy ammunition, ladies and gentlemen, because it’s going to be hard to get”.
The video was seen by US outlets but Mr Caputo’s account was later shut down. The issue of the coronavirus response has become highly politicised within Washington, with Mr Trump himself undercutting some of his top health advisers’ in a bid to reopen the country.
Democrats, in turn, have accused the Trump administration of sidelining experts in its messaging on the pandemic. A committee in the Democrat-controlled House of Representatives has launched an investigation into whether political appointees have meddled with official coronavirus data to better align with Mr Trump’s public statements.
The panel is requesting interviews with seven officials from the CDC and the Department of Health, including Mr Caputo.
According to a report in Politico, Mr Caputo, along with scientific adviser Paul Alexander, pressured officials to alter the CDC’s Morbidity and Mortality Weekly Reports (MMWR), a long-running weekly journal that features the latest science-based research and data on infectious diseases.
The officials pressured CDC to change the reports, at times retroactively, to better align them with Mr Trump’s often rosier public statements about the coronavirus, Politico reported.
The House panel is also demanding documents from the department, including communications sent or received by Health and Human Services Secretary Alex Azar, CDC Director Robert Redfield, Mr Caputo and Mr Alexander regarding the MMWR.
According to Politico, Mr Caputo and Mr Alexander complained about a report that explained children can transmit the coronavirus and Mr Alexander asked the CDC to alter it or pull it down, saying the report could impact school reopening and hurt Mr Trump politically.
In a statement on Monday night, the Department of Health and Human Services said “Mr Caputo is a critical, integral part of the President’s coronavirus response, leading on public messaging as Americans need public health information to defeat the COVID-19 pandemic.”