Researchers analysed data based on 1400 drug samples in five classes from seven Southeast Asian countries to reach to this conclusion.
Malaria is endemic in 106 countries. The disease claims 2500 lives worldwide every day.
A third of samples in sub-Saharan Africa failed chemical testing because they contained either too much or not enough active ingredient.
More than 3 billion people worldwide are at risk of malaria, a mosquito-borne parasitic disease which kills around 650,000 people a year, most of them babies and children in Africa.
Nayyar said many of the deaths caused by the disease could be avoided "if drugs available to patients were efficacious, high quality, and used correctly."
The World Health Organisation (WHO) estimates that while less than 1 percent of medicines available in developed countries are likely to be counterfeit, globally, the figure is around 10 percent.
The United Nations agency estimates that as much as a third of all medicines in some developing countries is fake.
As well as putting patients at risk, counterfeit drugs are a constant bane for companies like GlaxoSmithkline, Sanofi and other international drugmakers.
Nayyar's team analysed data from both published and unpublished studies that looked at chemical analyses and the packaging of malaria medicines in sub-Saharan Africa and southeast Asia where the malaria risk is highest.
Data from seven countries in southeast Asia - including from analysis of 1,437 samples of seven different malaria drugs - showed that more than a third of them failed chemical testing, nearly half were wrongly packaged, and about a third were bogus.
Analysis of data from 21 countries in sub-Saharan Africa including more than 2,500 drug samples, showed similar results, with more than a third failing chemical testing and around one fifth turning out to be fake.
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