WHO noted on Tuesday that a 2001 study in Southeast Asia's Mekong region showed that more than one-third of anti-malaria artesunate products in Cambodia, Laos, Myanmar, Thailand and Vietnam contained no active ingredients.
The situation worsened last year, with 99 out of 188 samples found to be counterfeit.
Fake drugs are estimated to generate more than $35 billion in sales a year, WHO said; and the problem is most serious in developing countries.
The Rapid Alert System, to be launched this week in Manila, will transmit reports on the distribution of fake medicine to national authorities so they can take rapid action.
"We hope that the Rapid Alert System will considerably strengthen our hand against the counterfeiters," said Budiono Santoso, WHO's regional adviser in pharmaceuticals for the western Pacific region.
"Rapid communication and efficient exchange of information are crucial to combating counterfeiting."
The agency said national health authorities and other partners would be linked to the system.