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The Southeast Asian nation calculated a palm oil reference price of 2,421.19 ringgit ($611.41) per tonne for June. Any price above 2,250 ringgit incurs a tax.
Malaysia resumed export taxes on crude palm oil in May at a 5 percent rate, after suspending it for four months at the start of the year to increase demand and boost prices.
Palm oil's benchmark prices were last trading down 0.7 percent at 2,718 ringgit on Wednesday afternoon.