"I’ve had conversations, and I’ve raised my concerns and I will continue to raise my concerns,” Gottlieb told CNBC's Squawk Box.

Gottlieb said he's enlisting Republican senators in his cause to sink RFK Jr.'s nomination using three core arguments: Large agricultural interests who could spend big against incumbent Republicans in future elections due to RFK Jr.'s positions on the American food industry, his past support for abortion rights and his opposition to childhood vaccines ruffling the feathers of "public health-minded" senators.

He's also warning senators against weighing their confirmation vote by using their position to box RFK Jr. in by threatening to withhold appropriations for HHS. He pointed out that Congress already has immense difficulty in passing government funding bills and doubted that there would political will in a Republican-controlled Congress to deny funding to a Republican executive branch.

"That's not going to be successful," Gottlieb said.

The former FDA commissioner also warned that RFK Jr.'s calls to revamp childhood vaccines could bring back a resurgence of measles and could "cost lives" if he takes the reins of HHS. RFK Jr.'s confirmation hearing will likely take place in the days following Trump's inauguration on January 20, 2025.