Two prominent scientists said in whistle-blower complaints filed late Wednesday that they had been removed from leadership positions at the National Institutes of Health after objecting to Trump administration efforts to undermine vaccines, flout court orders, withhold research money and politicize the grant-making process.

The complaints shed light on much of the internal strife at the agency earlier this year, as the Trump administration clamped down on the country’s medical research funding apparatus.

The scientists drew particular attention to what they described as an administration-wide “hostility” toward vaccines that they said had taken hold in the upper echelons of the N.I.H., long one of the world’s leading engines of vaccine research.

The allegations added to a growing chorus of protest from former high-ranking health officials over what they warned were dangerous and unscientific views about vaccines gripping the federal government and potentially opening the door to preventable infections.

Those policies have not only restricted people’s access to vaccines, some officials have said, but also have constrained federally funded research on future inoculations against infectious diseases.

The complaints were filed by Dr. Jeanne Marrazzo, who until the end of March had directed the National Institute of Allergy and Infectious Diseases, the institute previously run by Dr. Anthony S. Fauci; and Dr. Kathleen Neuzil, who until mid-April had directed the N.I.H.’s Fogarty International Center, which supports global health research.