Government spokesman Wichainchot Sukchotrat said Malaysian agriculture minister Mustafa Mohamed met with Thai Prime Minister Samak Sundaravej on Thursday to discuss the deal.
"Malaysia seeks an emergency purchase as a precaution to avert a rice shortage," Wichainchot told reporters.
"Thailand will help by sending at least 100,000 tonnes or up to half the requested amount by today."
The rest will be sent within the next three days, he said, adding that Thailand would sell the rice at market price.
As Malaysia seeks to protect its rice supply, it has said it is considering blocking the movement of the subsidised commodity across its borders.
Malaysia, which produces 70 percent of its rice needs and imports the rest from Thailand, heavily subsidises more than 20 daily food items, including milk and salt.
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World rice prices have soared this year, a trend blamed on higher energy and fertiliser costs, greater global demand, droughts, the loss of rice farmland to biofuel plantations, and