They called on the WHO to act amid fears that vulnerable patients are dying after turning to homeopathic preparations instead of effective medicines.
In the letter, early career medics and researchers from the Voice of Young Science network highlight homeopathy projects in Kenya, Tanzania, Ethiopia, Ghana and Botswana that all offer to treat patients with HIV, malaria, diarrhoea or the flu.
Homeopathy practitioners have opened clinics throughout Asian and sub-Saharan Africa and offer to treat patients with HIV, malaria, influenza and childhood diarrhoea, none of which have been shown to respond to homeopathy. Many patients are told that conventional drugs work only temporarily and that homeopathic preparations are cheap and effective alternatives with fewer side effects.
"Those of us working with the most rural and impoverished people of the world already struggle to deliver the medical help that is needed. When homeopathy stands in place of effective treatment, lives are lost," the scientists write in an open letter to the organisation.
Homeopathic medicines are made by repeatedly diluting preparations with water until there is no trace left of the original compound. The overwhelming medical opinion is that homeopathic treatments are no more effective than placebos, they contend.
Many people in developing countries urgently need access to evidence-based medical information and to the most effective means of treating these dangerous diseases. The promotion of homeopathy as effective or cheaper makes this difficult task even harder. It put lives at risk, undermines conventional medicine and spreads misinformation, the letter says.
"The WHO's strategy is very unclear on homeopathy and that is shocking. They are supposed to be articulating evidence-based medicine, but their stance is very wishy-washy," said Dr Daniella Muallem, a biophysicist at University College London, who signed the letter.
"Homeopathy is cheap, but there is no evidence that it works for these diseases, and the way they are being sold by practitioners is dangerous and completely unethical. There are medicines that do work and we should be advocating trying to get those to people," Muallem added.
According to WHO estimates, 33 million people were living with the HIV virus at the end of 2007, and during that one year, 2 million people died of Aids, including 270,000 children. Two-thirds of the world's HIV cases are in sub-Saharan Africa.
The organisation recorded 247 million cases of malaria and nearly 1 million deaths in 2006. A child dies of the disease every 30 seconds.
It works with national organisations that promote homeopathy and other alternative medicines in their public health programmes.
Some experts point to the South African example where hundreds of thousands of lives were lost consequent on the previous President Thabo Mbeki's flawed policies on HIV/AIDS. The catastrophe should not be repeated elsewhere, they stress.
During most of his presidency, Thabo Mbeki did not believe that HIV causes AIDS. Mbeki viewed AIDS as some kind of a Western conspiracy and "another Western characterization of Africans as promiscuous and Africa as a continent of disease and hopelessness."
In a speech in 2001, Mbeki said that the Western world sees Africans as "promiscuous carriers of germs, unique in the world... they [the West] proclaim that our continent is doomed to an inevitable mortal end because of our unconquerable devotion to the sin of lust."
A Harvard School of Public Health study said 330,000 deaths were caused by his 1999 decision to declare available drugs toxic and dangerous. Nearly 35,000 babies were also born HIV-positive between 2000 and 2005.
The former president had failed to roll out the drugs which could have prevented mother-to-child transmission, said the researchers.
The study, led by Dr Pride Chigwedere, accused the South African government of "acting as a major obstacle in the provision of medication to patients with Aids".
South Africa is experiencing one of the world's worst devastations caused by HIV/AIDS epidemic. AIDS is killing about 1,000 people a day in the country where more than five million of people, about 12% of the population, are infected with the virus. More than 2 million people have already died and one in eight of the working-age population is infected with HIV.