A senior Malaysian minister said the talks would cover issues such as timber requirements and standards, safety, environment and illegal logging.
Plantations minister Datuk Peter Chin said Malaysian timber producers still faced obstacles as some buyers were reluctant to use red meranti on reports it was non-durable.
It will be the first time the EU has worked on a formal agreement with any country based on a strict criteria of sustainability, legality and traceability involving the timber trade.
The talks are being conducted as part of the Forest Law Enforcement, Governance and Trade action plan.
The EU is the biggest market for Malaysian sawn timber ahead of Japan and the US.
