The Sudanese government said on Monday that it was not informed in advance of the meeting between Prime Minister Binyamin Netanyahu and the chairman of the Sovereignty Council of Sudan, Abdel Fattah Abdelrahman Burhan.
Sudan’s information minister and government spokesman, Faisal Salih, told Reuters he had no information about the visit and that the cabinet had not discussed it.
"We received the news about the meeting between chief of the sovereign council and Israeli prime minister through the media," Salih said in a later statement quoted by AFP.
"We, the members of the cabinet, were not notified or consulted about this meeting. We are waiting for the chief of the sovereign council to return and give clarification about this,” he added.
Netanyahu and the Sudanese leader met in Entebbe at the invitation of Ugandan President Yoweri Museveni.
During the meeting, it was agreed to start cooperation that will normalize relations between the two countries.
Burhan reportedly expressed his desire that his state go through a process of modernization by removing it from isolation and placing it on the world map.
A statement from Netanyahu's office following the meeting said the two men had "agreed to start cooperation leading to normalization of the relationship between the two countries".
It added that the prime minister believed "Sudan is headed in a new positive direction" and that he had expressed this view to US Secretary of State Mike Pompeo.
"Burhan is eager to help his country modernize by taking it out of isolation and putting it on the world's map," it said.
Burhan heads the Sovereignty Council which leads Sudan since the ousting of former dictator Omar al-Bashir last year.
The US in December lifted Sudan from a blacklist for religious freedoms violations, but still labels it a state sponsor of terrorism.
Israel and Sudan have had no formal ties in the past. In 2016, the country’s then-Foreign Minister hinted that his country could consider normalizing ties with Israel, but the government was then quick to that his comments were “taken out of contest”.