The debate - which focuses on hydrogen produced from nuclear or renewable energy - has already delayed negotiations on new EU renewable energy targets and threatened a multi-billion-euro hydrogen pipeline.
Some EU officials fear it could spill into other green energy policies, potentially delaying laws needed to meet EU climate targets.
"There are outstanding obstacles, but they will be resolved," EU foreign policy chief Josep Borrell said of the climate conclusions on Monday, without specifying what the obstacles were.
A draft of the conclusions, seen by Reuters, said: "EU energy diplomacy will promote the increasing uptake and system integration of renewable energy, hydrogen and its derivatives."
They says they acknowledge nuclear's low-carbon contribution, but that it should not be put on a level footing with renewable energy sources like wind and solar.