ATS are the second most used recreational drugs in the world, after cannabis, and the use of amphetamines continues to grow.
Smoking, sniffing and inhaling are the most popular methods of ATS use, but ways to take the drug vary widely across the region.
The study of amphetamine use in 11 countries in southeast Asia found those who injected the drugs were more at risk of contracting a blood-borne virus.
Other users are at higher risk of contracting HIV due to higher-risk behaviour, such as unsafe sex.
"Use appears higher among groups vulnerable to HIV such as sex workers, men who have sex with men, and young people," said the report, by the Australian National Council on Drugs (ANCD) in co-operation with the Asia-Pacific Drugs and Development Issues Committee.
ANCD chairman John Herron said the report highlighted the need for governments to take action.
"The effects of amphetamine-type stimulant use on young people cannot be underestimated," Herron was quoted as saying by Australian news agency AAP.
"Drug use may negatively impact on schooling and employment opportunities and contribute to risky behaviour - especially risky sexual behaviour among young people."
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