The conflict since April between Sudan's regular army and Rapid Support Forces, RSF, paramilitary has destabilized the western region and reignited long-simmering feuds there.
The EU's chief diplomat Josep Borrell cited in a statement witness reports that more than 1,000 members of the Masalit community were killed in Ardamta, West Darfur, in just over two days during attacks by the RSF and affiliated militias.
"These latest atrocities are seemingly part of a wider ethnic cleansing campaign conducted by the RSF with the aim to eradicate the non-Arab Masalit community from West Darfur, and comes on top of the first wave of large violence in June," Borrell said.
"The international community cannot turn a blind eye on what is happening in Darfur and allow another genocide to happen in this region."
On Thursday, the International Organization for Migration, IOM, said approximately 700 people were reportedly killed in West Darfur after clashes between the Sudanese army and RSF in El Geneina on Nov. 4 and 5.
The RSF said last week it had taken control of the army headquarters in West Darfur's capital of El Geneina.
Reuters has reported that between April and June this year, the RSF and allied Arab militias conducted weeks of systematic attacks targeting the Masalit, El Geneina's majority tribe, as war flared with Sudan's army.
In public comments, Arab tribal leaders have denied engaging in ethnic cleansing in El Geneina, and the RSF has previously said it was not involved in what it called tribal conflict.