The European Parliament adopted the new legislation in April that will ban imports deemed to be driving deforestation, throwing the bloc's trade muscle behind a global fight against climate change.
The law, which is awaiting final approval from EU member countries, would restrict imports from around the world on coffee, cocoa, soy, timber, palm oil, cattle, printing paper and rubber.
Imports that come from land deforested after December 31, 2020, will be prohibited in the huge EU market -- the third-largest for both Indonesia and Malaysia.
"Do not let the commodities produced by Malaysia and Indonesia be discriminated by other countries," Widodo said at a joint press conference alongside Malaysian Prime Minister Anwar Ibrahim.
"We need to continue to strengthen this collaboration," he said after the two leaders met in Malaysia's administrative capital Putrajaya.
Indonesia accounts for more than half the global supply of the edible oil, used in making foods such as cakes, chocolate, and margarine as well as cosmetics, soap and shampoo.
However, palm oil is a controversial commodity, blamed by environmentalists for fuelling the destruction of rainforests in Malaysia and Indonesia, which together produce 85 percent of global output.
Green groups say the rapid expansion of plantations has destroyed rare animals' habitats, while there have been allegations of foreign workers being abused and mistreated on some estates.
Widodo said he "deeply appreciated" ongoing cooperation between the two countries, referencing a recent visit by Indonesian and Malaysian officials to Brussels to combat the EU deforestation law.
A joint statement issued after the two leaders met said they had agreed to "cooperate closely to address highly detrimental discriminatory measures against palm oil by the European Union."
"They underlined that the EU needs to promptly address such discriminatory measures and work towards a fair and equitable resolution," it added.
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