The agency used the ruse in targeting Osama bin Laden before the US raid that killed him in 2011.
Lisa Monaco, President Barack Obama's top counter-terrorism adviser, wrote to the deans of 13 public health schools last week, saying that the CIA has agreed it would no longer use vaccination programmes or workers for intelligence purposes.
The agency also agreed to not use genetic materials obtained through such programmes.
A Pakistani doctor, Shakil Afridi, provided polio vaccinations in the Pakistani city of Abbottabad as cover for his CIA-backed effort to obtain DNA samples from children at a compound where bin Laden was later killed during a 2011 raid.
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The health school deans were among a group of medical authorities who publicly criticised the CIA's use of the vaccination programme after it was disclosed by media accounts and Pakistan's arrest of Afridi as a CIA operative.
In her May 16 letter to the health school deans, Monaco said that the US "strongly supports the Global Polio Eradication Initiative and efforts to end the spread of the polio virus forever."
She added that CIA Director John Brennan committed in August 2013 that the agency would "make no operational use of vaccination programmes, which includes vaccination workers."
CIA spokesman Dean Boyd said Brennan "took seriously the concerns raised by the public health community, examined them closely, and took decisive action."
Monaco's letter was first disclosed in a report by Yahoo News.