Rwanda's intelligence chief Karenzi Karake, who was arrested at the Heathrow Airport on 20 June was reported to have travelled to the UK to meet with Britain's head of MI6 Alex Younger, according to sources, the BBC reported.
The meeting was scheduled to take place on 18 June but was cancelled at the last minute, the sources said.
The BBC said Whitehall sources have neither confirmed nor denied details of MI6's engagement with Karake.
BBC Newsnight's investigations correspondent Nick Hopkins said: "One of the things that became clear at the [court] hearing is that Karake's lawyers will be relying on the fact that he should have had diplomatic immunity – he was here on official business.
"So I am sure that they will be seeking from the Foreign Office some kind of confirmation that he was here to see is counterpart."
Hopkins said that the claim that Karake was due to meet Younger was embarrassing for the British government and that the Rwandans "feel such a sense of betrayal over this."
Karake has been granted a £1m bail by Westminster magistrates ahead of a full extradition hearing on October. He is being held at the Belmarsh high security prison in Woolwich, south east London.
He was arrested under a European Arrest Warrant on behalf of Spain. In 2008, Karake was indicted by a Spanish judge on allegations that the 54 year old had ordered political assassinations and massacres between 1994 and 1997.
A report by Human Rights Watch also accused Unamid (African Union – UN Mission in Darfur) troops under the leadership of Karake of killing an estimated 760 civilians in the Congolese town Kisangani while fighting Ugandan soldiers in 2000.
He is also accused of ordering the killing of three medics from the NGO Médicos del Mundo.