"We were informed by the Met Police on 20th of June that they had arrested general Emmanuel Karenzi Karake," a Foreign Office spokesman said today.
The police said the 54-year-old was arrested at Heathrow airport on Saturday by extradition officers and was due to appear in court in London on Thursday.
Rwanda's foreign minister slammed the arrest.
"Western solidarity in demeaning Africans is unacceptable!!" Foreign Minister Louise Mushikiwabo said on Twitter. "It is an outrage to arrest Rwandan official based on pro-genocidaires lunacy!"
A Spanish court seven years ago listed Karake in a roll-call of 40 army officers it intended to prosecute for genocide and crimes against humanity in Rwanda during the 1990s.
The court's decision followed an investigation into the murder of nine Spaniards in Rwanda between 1994 and 2000 who were working with refugees.
The Foreign Office declined to comment further on the arrest but said that Britain and Rwanda "have a deep, long-standing relationship with a wide range of shared interests".
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