Sheikh Mohamed bin Zayed met Lt Gen Abdel Fattah Al Burhan, head of Sudan's Sovereignty Council, who is on a working visit to the Emirates.
The Crown Prince of Abu Dhabi and Deputy Supreme Commander of the Armed Forces and his guest discussed relations between the two countries.
Sheikh Mansour bin Zayed, Deputy Prime Minister and Minister of Presidential Affairs, also attended the meeting at Al Shati Palace on Sunday.
The leaders exchanged views on regional and international issues, especially developments in the Horn of Africa.
They emphasised there was need to give "priority to the voice of wisdom, dialogue and finding diplomatic solutions to the various issues and challenges facing the region, in a way that contributes to defuse tensions and crises", state news agency Wam reported.
Sheikh Mohamed repeated the UAE's support for Sudan's efforts to promote peace, stability and development, especially during this critical phase of its history. Sudan's stability, security and safety represent an important pillar in the region's security, Sheikh Mohamed said.
Lt Gen Al Burhan said Sudan was keen to enhance various aspects of co-operation with the UAE.
He thanked the UAE for its position on preserving Sudan's stability and security during the challenges it is currently facing. He also praised the country's humanitarian initiatives and medical supplies it continues to provide to Sudan amid the global fight against Covid-19.
The meeting was attended by Sheikh Hamdan bin Mohamed bin Zayed; Khaled Omar Youssef, Sudan's Minister of Cabinet Affairs; and the accompanying delegation.
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