Infectious diseases are an issue of national security, but the global fight against them is threatened by allegations that US security agencies use vaccination programs for intelligence operations. In December 2012, ten polio vaccination workers in Pakistan and Afghanistan were shot, causing the Pakistan government to suspend a polio vaccination drive. The Taliban claim the polio eradication program is part of a US intelligence plot and that the vaccine itself is harmful to recipients. In September 2012, the Pakistan government itself ordered foreign employees of Save the Children to leave the country, saying they were part of a plot to use a hepatitis B vaccine campaign to collect intelligence. Save the Children denies the allegations.
The lower vaccination rates that result from allegations that programs are a cover for security operations damage broader US national security interests.
These are only the latest cases where allegations that a vaccination program was a front for US security operations have led to setbacks in the global battle against infectious disease. Efforts to contain a polio outbreak in Kano, Nigeria, in 2003 that might have put us on the path to global polio eradication were derailed when imams and local political leaders called for a boycott of the polio vaccination campaign. They claimed (without evidence) that the vaccine program was part of a US sterilization plot. Country coverage of full polio vaccination fell from
38 percent in 2000 to 32 percent in 2005,  the boycott led to a
30 percent spike in polio prevalence in the region,  and cases of polio
countrywide increased from 202 in 2002 to 1,143 in 2006. 
The lower vaccination rates that result from allegations that programs are a cover for security operations damage broader US national security interests related to global public health.President Clinton’s Presidential Decision Directive NSTC-7 determined that global infectious diseases were a significant threat to the health of US citizens and that the international system of disease surveillance, prevention, and response needed to be considerably strengthened with additional US support. In 2000, the National Intelligence Council released a
National Intelligence Estimate which concluded that “New and reemerging infectious diseases will pose a rising global health threat and will complicate US and global security over the next 20 years. These diseases will endanger US citizens at home and abroad, threaten US armed forces deployed overseas, and exacerbate social and political instability in key countries and regions in which the United States has significant interests.” 
Vaccination programs have already reduced child deaths in the developing world by millions each year—with knock-on effects in terms of stronger broad-based sustainable development that is of benefit to the United States. But the lower disease burden also has a direct impact on the health of Americans. In the case of polio, for example, it is only 60 years ago that tens of thousands of Americans were left paralyzed by an outbreak of the disease while three thousand died. Global eradication would free Americans from that threat forever. Regarding hepatitis B, according to the
Centers for Disease Control there were an estimated 38,000 new infections in 2010 in the US, and 3,000 people died of chronic liver conditions associated with infection.  The United States is particularly susceptible because it has a comparatively low vaccination rate against the disease: the 91 percent coverage rate reported to the World Health Organization ranks it 100th in the world. Lower international infection rates would reduce the risk of hepatitis B outbreaks in the United States. 
Given the vital importance of global child vaccination programs to US national security interests, and the chilling effect of allegations regarding links to US intelligence operations, intelligence-community use of child public health service provision as part of operations should be explicitly banned.
There are already legislative and executive constraints on intelligence agency activities that respond to conflicts between the national security interests furthered by intelligence operations and other national security or broader concerns.
Executive Order 13491 states that anyone in US custody “shall not be subjected to any interrogation technique or approach, or any treatment related to interrogation, that is not authorized by and listed in Army Field Manual 2 22.3 (Manual).” 
Executive Order 12333 bans employees of intelligence agencies from joining organizations in the United States on behalf of the intelligence community without disclosing their affiliation. It also mandates that “No element of the Intelligence Community shall sponsor, contract for, or conduct research on human subjects except in accordance with guidelines issued by the Department of Health and Human Services,” and bans engagement in or conspiracy toward assassination and actions intended to influence United States political processes, public opinion, policies, or media. 
The proposal here is to amend Executive Order 12333 to add a paragraph after the prohibition on covert action related to US domestic politics. The paragraph would read: “ 2.14 No person acting on behalf of elements of the Intelligence Community may join or otherwise participate in any activity directly related to the provision of child public health services on behalf of any element of the Intelligence Community.”
An explicit order regarding child public health campaigns might help restore confidence in vaccination programs.
It is of course doubtful that many of those in infected communities would know of any constraint on the use of vaccination programs by US intelligence services, or that the knowledge would be sufficient to reverse a decision against vaccination in any particular case. However, the constraint could be advertised to local politicians and community leaders as part of vaccination campaigns, potentially reducing the risk of a boycott. Furthermore, the decision to vaccinate is made by many millions of parents every year, so even a very small shift in decisions for or against vaccination at the individual level would impact many thousands of children worldwide. And the knock-on effects of a lower overall disease burden would benefit even those who remain unvaccinated.
In the spirit of existing constraints,an explicit order regarding child public health campaigns might help restore confidence in vaccination programs.President Obama should take the step of amendingExecutive Order 12333 for the sake of global child health and America’s own national security interests.