Israeli Intelligence Minister Eli Cohen led a delegation to Khartoum months after Sudan agreed to normalise relations.
Monday’s visit marked the first time an Israeli minister headed an official delegation to the North African state, Cohen’s office said on Tuesday.
Sudanese state media did not report the trip.
Israel’s intelligence ministry said in a statement that members of the delegation met the head of state, General Abdel Fattah al-Burhan, and Defence Minister Yassin Ibrahim for talks on “diplomatic, security and economic issues”.
“A first-ever memorandum on these topics was signed between the Sudanese defence minister and Cohen,” it said.
The sides also discussed “deepening intelligence cooperation”.
“The Sudanese authorities briefed the Israeli delegation on their progress on cancelling the law boycotting Israel, and amending the law imprisoning Sudanese migrants, including to Israel, who return to Sudan,” the ministry added.
The statement also said it was agreed that a Sudanese delegation will travel to Israel, but did not mention when.
Sudan agreed to normalise ties with Israel in October last year and an Israeli delegation visited Khartoum the following month.
On January 6, Sudan signed the “Abraham Accords” normalising ties with Israel, making it the third Arab country to do so after the United Arab Emirates and Bahrain last year.
Morocco also normalised its ties with Israel in December.
Khartoum signed the accords less than a month after Washington removed it from its “state sponsors of terrorism” blacklist as part of a quid pro quo.
But protests against normalisation have continued in Sudan. On January 17, dozens of protesters gathered outside the cabinet office in Khartoum and burned the Israeli flag.
Until last year, Egypt and Jordan were the only Arab countries to have recognised Israel, in bilateral peace deals struck decades ago.
Other Arab governments refused to normalise relations until Israel reached a comprehensive peace agreement with the Palestinians and its other neighbours.
Cohen said his visit to Khartoum “laid the foundations for many important collaborations that will help Israel and Sudan, boost regional stability, deepen our ties with Africa and lead to more agreements with states in the region”.