Representative Image. Photograph:( Zee News Network )
Netanyahu met Sudan's leader Abdel Fattah al-Burhan two weeks ago for what the Israeli premier's office described talks aimed at normalising ties.
An Israeli aircraft have flown through Sudanese airspace for the first time, in what Prime Minister Benjamin Netanyahu called another example of warming ties with formally hostile states.
Bashir was ousted by the army last April following months of mass anti-government demonstrations.
"The first Israeli aeroplane passed yesterday over the skies of Sudan. This is quite a change," Netanyahu told American Jewish leaders in Jerusalem on Sunday evening, without offering further details.
Israeli daily Haaretz quoted an Israeli government official, speaking on condition of anonymity, saying that the plane was "a private Israeli executive jet".
A Sudanese government spokesman said later that Burhan "did not give a promise of normalising or having diplomatic relations".
Sudan has been part of a decades-old Arab boycott of Israel over its treatment of the Palestinians and its occupation of Arab lands.
In the wake of the Six-Day War of 1967 in which Israel occupied the Palestinian territories and seized the Golan Heights from Syria, Arab leaders gathered in Khartoum to announce what became known as the "three nos": no peace, no recognition and no negotiations with Israel.
Netanyahu said Sunday that visible signs of a thaw in relations with Sudan and other Muslim-majority countries were only the tip of the diplomatic iceberg.
"How much is above the surface in an iceberg? It's about 10 per cent, he said. "What you're seeing is about 10 per cent. Vast changes are coming."
Gulf Arab countries have made a number of recent moves hinting at warmer ties with the Jewish state, prompted largely by a shared enmity towards Iran.
Netanyahu visited Oman in 2018 and he frequently says the boycott of his country is ending, despite the absence of a peace deal with the Palestinians.
Egypt and Jordan are so far the only Arab states to have full diplomatic relations with Israel.
Netanyahu was speaking two weeks ahead of a March general election, the third in 12 months. He has twice failed to form a government after inconclusive polls.