As he left Israel, Netanyahu said that he was "strengthening our relationship" with Uganda, and that he hoped to "have very good news for the State of Israel" from the trip. In 2015, Sudan's alleged downing of Israeli drone was also circulating among the press.
On Monday, Benjamin Netanyahu's office said he had met General Abdel Fattah al-Burhan, chairman of Sudan's ruling sovereign council, in the Ugandan city of Entebbe in a previously unannounced meeting.
Sudan is also trying to get off the USA list of state sponsors of terrorism. That would be a key step toward ending its isolation and rebuilding the economy after the popular uprising a year ago that toppled autocrat Omar al-Bashir and installed the joint civilian-military sovereign council, headed by Burhan.
US President Trump last week released a Israeli-Palestinian peace plan widely seen as skewed towards Israel.
In recent years, Israel has boosted its links with African nations, improving ties following a hard period when many post-independence African leaders sided with Israel's Arab rivals and viewed Israel's support for apartheid, South Africa, with intense suspicion.
The Palestinians have been seeking to build unified opposition among Arab nations in opposition to the plan, with the Arab League rejecting it on Saturday.
While the Israeli government and Israeli media widely circulated the news of the Burhan-Netanyahu meeting in Uganda, Sudanese outlets have been quiet about the news and the reasons behind such a radical change in Khartoum's long-standing foreign policy. The statement said Netanyahu "believes that Sudan is moving in a new and positive direction" - an apparent reference to a possible removal from the US terror list.
"This meeting is a stab in the back of the Palestinian people.at a time when the administration of President Donald Trump and Israeli Prime Minister Netanyahu are trying to liquidate the Palestinian cause", Saeb Erekat, secretary general of the Palestine Liberation Organization, said in a statement carried on official news agency WAFA.
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The two leaders agreed to work toward normalizing relations between their countries.
Israel now has diplomatic relations with 39 of 47 sub-Saharan African states. Burhan had been invited to Washington DC one day earlier.
In Sudan, the move met condemnation from the Communist Party, a prominent former member of Bashir's National Congress Party and other Islamist factions.
"We, the members of the cabinet, were not notified or consulted about this meeting", Salih said in a statement.
Netanyahu arrived in Uganda on Monday, saying Israel is "returning to Africa in a big way" and urging the East African country to open an embassy in Jerusalem.
"This is just another example of how ultimately Israel can create these ties and get along with Arab and Muslim countries".