EU rules in force since last year prohibit a vast range of goods -- from coffee to cocoa, soy, timber, palm oil, cattle, printing paper and rubber -- if produced on land deforested after December 2020.
Goods will be judged according to the bloc's ranking of the risk of associated deforestation, with Malaysia avoiding a "high risk" designation but failing to garner a "low risk" status that would have meant less stringent checks.
Instead it has been classed as "medium risk", along with countries including Brazil and neighbouring Indonesia.
Plantation and Commodities Minister Johari Abdul Ghani rejected the classification on Wednesday, saying it was based on 2020 United Nations Food and Agriculture Organisation data.
"Malaysia has implemented strict no-deforestation policies and developed our own certification system... which ensures traceability, compliance, and inclusivity, particularly for smallholders," Johari said in Singapore.
Malaysia is committed to working with the EU to "present updated, science-based evidence" to support its request for "low risk" status and "fair recognition of our progress", he added.
Only goods imported from Russia, Belarus, North Korea and Myanmar were labelled "high risk", over objections from environmentalists who argue rampant deforestation in other countries should mean extra scrutiny.
Malaysia is the world's second-biggest exporter of palm oil, behind only Indonesia, and both countries have pressed the EU over what they consider overly onerous compliance rules under the new anti-deforestation regulations.
Implementation of the rules was delayed after pressure from various countries.
From December, firms importing the affected commodities will be responsible for tracking their supply chains to prove goods did not originate from deforested zones, relying on geolocation and satellite data.
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