Sudan's leader General Abdel Fattah al-Burhan said Tuesday his meeting with Israeli Prime Minister Benjamin Netanyahu the previous day was driven by his responsibility to protect the country's national security.

Burhan's first remarks about the meeting in Uganda, talks that surprised even Sudan's cabinet, came after he briefed the northeast African country's ruling sovereign council which he heads.

"I took this step from the standpoint of my responsibility... to protect the national security of Sudan and achieve the supreme interests of the Sudanese people," Burhan said in a brief statement released after he met the council and top ministers.

Israel remains technically at war with Sudan, which supported hardline Islamists including Al-Qaeda during the decades-long reign of autocrat Omar al-Bashir, ousted amid mass protests last year.

The Palestinian leadership has denounced the meeting as "a stab in the back", just days after the Israeli leader and US President Donald Trump unveiled a controversial peace plan, widely seen as skewed towards Israel.

"I stress that examining and developing relations between Sudan and Israel is the responsibility of the concerned institutions, as according to (Sudan's) consitutional declaration" signed following Bashir's ouster, Burhan said.

"I also confirm that Sudan's principled stance on the Palestinian issue and the right of its people to an independent state is and will remain firm, in keeping with Arab consensus and Arab League resolutions."

Netanyahu's office said Monday that he and the Sudanese general had "agreed to start cooperation leading to normalisation of the relationship between the two countries".

Israeli Prime Minister Benjamin Netanyahu says he met the leader of Sudan during his visit to Entebbe in Uganda Israeli Prime Minister Benjamin Netanyahu says he met the leader of Sudan during his visit to Entebbe in Uganda Photo: AFP / SUMY SADURNI

It said Netanyahu believed post-Bashir Sudan is headed "in a new positive direction" and that he had also expressed this view to US Secretary of State Mike Pompeo.

"Burhan is eager to help his country modernise by taking it out of isolation and putting it on the world's map," it said.

The Uganda meeting came after Sudan said Pompeo had invited Burhan to Washington for an official visit, the first such invitation to a Sudan ruler in more than three decades.

The United States still classifies Sudan as a state sponsor of terrorism, a legacy from the rule of Bashir who in the 1990s hosted Osama bin Laden.

President of Sudan's Transitional Council Abdel Fattah al-Burhan pictured last November President of Sudan's Transitional Council Abdel Fattah al-Burhan pictured last November Photo: AFP / Michael O'HAGAN

Late on Monday, Sudanese government spokesman Faisal Mohamed Salih said the cabinet had only learned of the meeting at Entebbe through media reports.

"We, the members of the cabinet, were not notified or consulted about this meeting," Salih said in a statement.

Sudan under Bashir was part of the decades-long Arab boycott of Israel over the Jewish state's treatment of the Palestinians and occupation of Arab lands.

In the wake of the 1967 war in which Israel captured Palestinian lands, Arab leaders held a historic meeting in Khartoum to announce what became known as the 'three nos' -- no peace, recognition or negotiations with Israel.

Since then, Egypt and Jordan have recognised Israel, and relations have been easing between Israel and Gulf Arab states in part due to shared concern over Iran's role in the region.

The Palestinians have been seeking a united front since Trump last week unveiled his Middle East plan.

The initiative gave the Jewish state the US green light to annex settlements in the occupied West Bank, as well as the Jordan Valley, a key territory Palestinians see as their future state.

The Palestine Liberation Organization called Burhan and Netanyahu's meeting "a stab in the back of the Palestinian people".

In a statement carried on official news agency WAFA, the organisation's chief Saeb Erekat accused Washington and Netanyahu of "trying to liquidate the Palestinian cause".

The Sudanese Communist Party, which is part of the umbrella protest movement that led to the ouster of Bashir last April, echoed that condemnation.

"What happened at the meeting between Burhan and Netanyahu is a stab in the back of Sudanese people's struggle against imperialists and also their continuous position in supporting the Palestinians," party spokesman Fathi Fadoul said in a video broadcast on the party's Facebook page.

"We also condemn the statement from the cabinet. The cabinet has to say directly what its position is about the meeting rather than saying it was not notified about it."