"This is a difficult situation. It's a fast-moving situation, and we will continue to work on it," European Commission spokesman Eric Mamer said.
He was responding to the investigation published by Lighthouse Reports in collaboration with outlets including Le Monde and The Washington Post.
The report said: "Europe supports, finances and is directly involved in clandestine operations in North African countries to dump tens of thousands of black people in the desert or remote areas each year to prevent them from coming to the EU."
It described a "system of mass displacement" that was "run thanks to money, vehicles, equipment, intelligence and security forces provided by the EU and European countries."
The report said refugees and migrants in Morocco, Mauritania and Tunisia were being "apprehended based on the color of their skin, loaded onto buses and driven to the middle of nowhere, often arid desert areas," without water or food.
Others reportedly were taken to border areas where they were allegedly "sold by the authorities to human traffickers and gangs who torture them for ransom."
The 27-nation EU has struck cooperation deals with the three named countries that include explicit financing to boost their abilities to curb irregular migration to Europe.
Brussels has allocated 150 million euros ($160 million) to Tunisia, 210 million euros to Mauritania and 624 million euros to Morocco under these cooperation agreements.
Racially motivated practices
The EU's efforts to have African countries stem migration flows across the Mediterranean Sea go hand in hand with a newly agreed overhaul of the bloc's asylum rules.
These will make EU borders tighter and speed up the deportation of unsuccessful asylum seekers.
The Lighthouse Reports said it interviewed more than 50 black migrants — all of them from sub-Saharan Africa and West Africa — who had been expelled from the three North African countries.
Their testimony, including videos and photos, "helped us to recognise the systematic and racially motivated nature of the practices," along with the consortium's own evidence gathering, it said.
It cited unnamed European officials as denying that EU funds were being used to violate migrants' rights.
But it said two EU sources acknowledged it was "impossible" to fully account for how the funding from Brussels was being used.
The European Commission — the EU's executive arm — did not respond explicitly to the report's allegations.
Commission spokeswoman, Ana Pisonero, said: "Sometimes the situation is challenging in our partner countries... (but they) remain sovereign states and they continue to be in control of their national forces."
She said the EU monitored programs it provided funding for, and noted pledges from partner countries to uphold international law and human rights.
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