The agency's efforts will begin later this year and will build on its success in tackling the problem in Latin America and Southeast Asia, said John Newton, the manager of Interpol's intellectual property rights project.
"We have learned a lot of lessons in those regions and we are now able to apply those to Africa," he told AFP on the sidelines of Interpol's annual general assembly in Marrakech in southern Morocco.
Congo, Nigeria, Senegal and Sudan asked the 186-member police body at the gathering for for help in stopping smuggling networks from making fake drugs readily available in their markets and sometimes even pharmacies, he said.
"The Africans are very keen for Interpol to work with them on this subject," said Newton.
Interpol will train police in Africa on how to smash counterfeit medicine smuggling networks, coordinate police operations and track the flow of fake drugs from southeast Asia and other parts of the world to the continent.
As it has in other regions, the global police body will work with the World Health Organization and drug companies to tackle the problem.
"We can bridge the gap between law enforcement and the public health sector, we are able to bring the two areas together," said Newton.
The World Health Organization estimates that up to 30 percent of the medicine sold in Africa is fake.
Counterfeit medicine networks take advantage of Africa's poor or non-existent drug regulatory systems to dump drugs with little or no active ingredient in the continent, experts say.
Interpol carried out its first-ever operation solely dedicated to the trade in fake medicine in 2005 in seven southeast Asian countries.
"We are concerned about counterfeit medicines for life-threatening diseases such as malaria, tuberculosis and HIV/AIDS and increasingly getting involved in this area," said Newton.
The US-based Center for Medicines in the Public Interest estimates that global counterfeit drug sales will rise to 75 billion dollars by 2010, a 90 percent increase over 2005.