Rwanda’s intelligence chief Karenzi Karake, who is wanted in Spain for war crimes, has been arrested in London, BBC Newsnight has learned.

It is understood the Met Police’s extradition unit arrested Gen Karake at Heathrow Airport on Saturday.

Scotland Yard confirmed the Rwandan had appeared before Westminster Magistrates’ Court after being detained under a European Arrest Warrant.

The 54-year-old was remanded in custody until Thursday.

Newsnight understands the Rwandan government is puzzled by the timing of Gen Karake’s arrest as he had travelled to the UK several times since the indictment was issued.

A source told the programme that Gen Karake’s detention would be contested vigorously.

Gen Karake is director general of Rwanda’s National Intelligence and Security Services.

In 2008, a Spanish judge indicted him for alleged war crimes.

He is accused of ordering a number of massacres while head of military intelligence after the 1994 genocide in Rwanda.

An estimated 800,000 Rwandans were killed between April and June 1994 by ethnic Hutu extremists.

Most of the dead were members of the minority Tutsi community and politically moderate Hutus.

The killings ended when the Rwandan Patriotic Front (RPF), a Tutsi-led rebel movement that entered Rwanda from Uganda, seized control of the country.

Gen Karake, who is a member of the RPF, is one of 40 current or former high-ranking Rwandan military officials named on the Spanish indictment.

He is also accused of ordering the killing of three Spanish nationals working for Medicos del Mundo.

Phillip Gourevitch, a leading writer on Rwanda, told Newsnight that Gen Karake’s arrest was the equivalent of the head of the UK’s MI6 or the US’s CIA being arrested.

He said the Spanish indictment against Gen Karake and 39 others had been criticised as highly politicised by many, including US diplomats.