Authorities ordered schools in the states of Perlis and Pahang to shut after temperatures soared above 37 degrees Celsius (98.6 degrees Fahrenheit) over a 72-hour period, according to local reports.
The education ministry said the decision was made to protect the health of some 100,000 students, the official news agency Bernama reported.
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Paddy fields and rubber plantations have been also been affected by the severe temperature rise.
January and February 2016 smashed global temperature records, the World Meteorological Organisation said in March, attributing the highs to the "unprecedented" advance of climate change.
Many parts of Asia have been affected by the strong El Nino dry spell which has also hit agriculture in Thailand and the Philippines.
El Nino is triggered by a warming in sea surface temperatures in the Pacific Ocean. It can cause unusually heavy rains in some parts of the world and drought in others.
But Malaysia's Meteorological Department said the current heatwave was expected to ease soon.
"The worst is over because the inter-monsoon season started last week and more rain is expected," director-general Che Gayah Ismail said.
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