The official warned that donor countries could be considered complicit in any possible crimes if they do nothing to stop them.
The warning was made in an urgent memo to Eric van der Linden, the EU ambassador based in Nairobi, Kenya.
The author, whose name was blanked out on the copy obtained by The Associated Press, went on to detail the exact statutes that they believed may have been violated.
The official's email said: "I need to advise you that there are strong grounds to believe that the Ethiopian government and the transitional federal government of Somalia and the African Union (peacekeeping) Force Commander, possibly also including the African Union Head of Mission and other African Union officials have through commission or omission violated the Rome Statute of the International Criminal Court.
"In regard to the above mentioned potential violations of international law there arise urgent questions of responsibility and potential complicity in the commission of war crimes by the European Commission and its partners."
Solomon Abebe, spokesman for the Ethiopian ministry of foreign affairs, called the allegations a "fabrication".
Abebe said: "The international community, everybody knows that this is false."
EU officials were not immediately available for comment because Friday was a public holiday in Kenya. Somali officials were unreachable.
European diplomats said they were concerned about the information.
Jens Orlander, the Swedish special envoy for Somalia based in Nairobi, said: "We are looking at this from a legal point of view at the ministry of foreign affairs in Stockholm."
Güncelleme Tarihi: 20 Eylül 2018, 18:16