The White House has pledged the CIA will not use immunization programs as a cover for spying operations.
Lisa Monaco, President Barack Obama's top counterterrorism adviser, wrote to the deans of 13 prominent health schools to say the CIA had pledged not to use vaccination programs for intelligence purposes.
The deans had criticized the CIA's use of the vaccination program after it was disclosed by media accounts and the arrest of a Pakistani doctor as a CIA operative.
Shakil Afridi was sentenced by a Pakistani court to 33 years in prison for treason for offering a program of hepatitis vaccinations as part of an alleged CIA-backed effort to obtain DNA samples from children at a compound where Osama bin Laden was later killed during a U.S. raid.
The sentence was overturned and Afridi faces a retrial.
A spokesman said CIA Director John Brennan had taken "decisive action" after concerns were raised.
Based on reporting by AP and Reuters