It did not say when the change would take place, but said it was part of a strategy aiming to prevent underage drinking and limit the accessibility of alcohol to high risk groups.
Malaysia also plans additional labelling requirements for alcohol products to warn about their effect on health, it said.
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The filing to the WTO invites other members of the global trading body to comment on its plans within the next 60 days.
Malaysia is a predominantly Muslim country but also home to Carlsberg Brewery Malaysia Bhd, which reported an 11 percent increase in quarterly profits on Monday, and Guiness Anchor Bhd,
Alcohol is widely available and consumed by an estimated 3.5 million of the nearly 30 million population, according to the Confederation of Malaysian Brewers Berhad.
The country already has one of Asia's highest excise taxes on alcohol, but consumption of alcohol has been relatively steady.
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In neighbouring Indonesia, which has the world's largest Muslim population, lawmakers have proposed legislation to ban all consumption of alcoholic drinks and hand jail terms of up to two years to offenders.
It also introduced a steep increase in import tariffs on wine and spirits.
Last year, Malaysia exported spirits worth $269 million, mainly to Singapore, Vietnam and Thailand, and beer worth $156 million, mainly to Singapore and Thailand.
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