In 1959, the WHO signed Agreement WHA 1240 with the International Atomic Energy Agency (IAEA). The agreement states that the WHO recognises the IAEA as having responsibility for peaceful nuclear energy without prejudice to the roles of the WHO of promoting health. However, the following paragraph adds: "whenever either organization proposes to initiate a programme or activity on a subject in which the other organization has or may have a substantial interest, the first party shall consult the other with a view to adjusting the matter by mutual agreement".[92] The nature of this statement has led some pressure groups and activists (including Women in Europe for a Common Future) to believe that the WHO is restricted in its ability to investigate the effects on human health of radiation caused by the use of nuclear power and the continuing effects of nuclear disasters in Chernobyl and Fukushima. They believe WHO must regain what they see as "independence

In 2003, the WHO denounced the Roman Curia's health department's opposition to the use of condoms, saying: "These incorrect statements about condoms and HIV are dangerous when we are facing a global pandemic which has already killed more than 20 million people, and currently affects at least 42 million."[96] As of 2009, the Catholic Church remains opposed to increasing the use of contraception to combat HIV/AIDS.[97] At the time, the World Health Assembly President, Guyana's Health Minister Leslie Ramsammy, condemned Pope Benedict's call,[clarification needed] saying he was trying to "create confusion" and "impede" proven strategies in the battle against the disease The aggressive support of the Bill & Melinda Gates Foundation for intermittent preventive therapy of malaria which included the commissioning of a report from the Institute of Medicine triggered a memo from the former WHO malaria chief Akira Kochi Some of the research undertaken or supported by WHO to determine how people's lifestyles and environments are influencing whether they live in better or worse health can be controversial, as illustrated by a 2003 joint WHO/FAO report on nutrition and the prevention of chronic non-communicable disease,[100] which recommended that sugar should form no more than 10% of a healthy diet. This report led to lobbying by the sugar industry against the recommendation, to which the WHO/FAO responded by including in the report the statement "The Consultation recognized that a population goal for free sugars of less than 10% of total energy is controversial", but also stood by its recommendation based upon its own analysis of scientific studies. In 2007, the WHO organized work on pandemic influenza vaccine development through clinical trials in collaboration with many experts. A pandemic involving the H1N1 influenza virus was declared by Director-General Margaret Chan in April 2009. By the post-pandemic period critics claimed the WHO had exaggerated the danger, spreading "fear and confusion" rather than "immediate information".[102] Industry experts countered that the 2009 pandemic had led to "unprecedented collaboration between global health authorities, scientists and manufacturers, resulting in the most comprehensive pandemic response ever undertaken, with a number of vaccines approved for use three months after the pandemic declaration. This response was only possible because of the extensive preparations undertaken in during the last decade"