Sudan's Bashir moved to military hospital before fighting: sources
The whereabouts of Bashir came into question after a former minister in his government, Ali Haroun, announced on Tuesday he had left the prison with other ex officials.
Both Bashir and Haroun are wanted by the International Criminal Court over alleged atrocities in Darfur.
Fighting flared anew in Sudan late on Tuesday despite a ceasefire declaration by the warring factions as more people fled Khartoum in the chaos.
The Sudan Armed Forces (SAF) and paramilitary Rapid Support Forces (RSF) agreed to a 72-hour ceasefire beginning on Tuesday after negotiations mediated by the US and Saudi Arabia.
But gunfire and explosions could be heard after nightfall in Omdurman, one of Khartoum's sister cities on the Nile River where the army used drones to target RSF positions, a Reuters reporter said.
UN special envoy on Sudan Volker Perthes told the UN Security Council on Tuesday that the ceasefire "seems to be holding in some parts so far".
But he said that neither party showed readiness to "seriously negotiate, suggesting that both think that securing a military victory over the other is possible".
"This is a miscalculation," Perthes said, adding that Khartoum's airport was operational but the tarmac damaged.
The first Turkish civilians evacuated from Sudan returned to Turkey on Wednesday and Saudi Arabia said it evacuated 13 of its nationals and 1,674 other individuals with no sign the warring parties are ready to seriously negotiate.
The Turks came from the Ethiopian capital Addis Ababa, having reached there overland from Khartoum.
Several more flights were expected later on Wednesday to evacuate the remaining Turkish citizens who had crossed over to Ethiopia from Sudan.