WASHINGTON — Three years after the Central Intelligence Agency set up a phony hepatitis vaccination program in Pakistan as part of the hunt for Osama bin Laden, the Obama administration told a group of American health educators last week that the agency no longer uses immunization programs as a cover for spying operations.

In a letter to leaders at a dozen schools of public health, President Obama’s senior counterterrorism adviser said the C.I.A. had banned the practice of making “operational use” of vaccination programs, adding that the agency would not seek to “obtain or exploit DNA or other genetic material acquired through such programs.”

The letter from the adviser, Lisa O. Monaco, comes more than a year after public health officials wrote to Mr. Obama expressing anger that the United States had used immunization programs as a front for espionage. The educators were protesting the C.I.A.’s employment of a Pakistani doctor, Shakil Afridi, to set up a hepatitis B vaccination program in Abbottabad to gain access to a compound where Bin Laden was believed to be hiding.

“While political and security agendas may by necessity induce collateral damage, we as a society set boundaries on these damages, and we believe this sham vaccination campaign exceeded those damages,” the educators’ letter said.