On his arrival, several civil society groups approached an Abuja High Court demanding the arrest of the president who has been indicted by the International Criminal Court.
The Hague-based ICC has issued two warrants against Bashir for war crimes, crimes against humanity and genocide over the conflict in Sudan's Darfur region.
According to Sudanese officials, al-Bashir left Nigeria yesterday. He had arrived on Sunday.
Nigerian Foreign Minister Ambassador Olugbenga Ashiru told PTI that the Sudanese head of state was in Nigeria at the instance of the African Union.
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The ICC had urged Nigeria to arrest the Sudanese leader while the United States and the UK expressed their displeasure over his being allowed to arrive in the country.
Nigeria gave him the privilege of inspecting a guard of honour before appearing at the venue of the summit. The essence of the summit was also overshadowed by his appearance.
High Commissioner of India to Nigeria Mashesh Sachdev was invited by the AU as one of the special observers at the summit which lasted for two days.