A video circulating on social media on Saturday showed Egypt's foreign minister Sameh Shoukry removing an Al Jazeera microphone from the table in front of him as he was about to address a press conference in Khartoum.
In July 2013, shortly after Islamist president Mohamed Morsi was ousted, Egypt closed the Cairo office of the Qatari network, accusing it of biased and unprofessional coverage.
The Qatari network has continuously attacked the post-Morsi government, accusing it of undemocractic practices.
Egypt says Al Jazeera spreads false information about reality on the ground in the country.
In 2015, President Abdel-Fattah El-Sisi ordered the release of two Al Jazeera journalists, Mohamed Fahmy and Peter Greste, who had been convicted of reporting false news, and had been in jail since December 2013.
Relations between Egypt and Qatar soured after the ouster of Morsi, a key ally of Doha.
Shoukry was in Khartoum to take part in trilateral talks on the Grand Ethiopian Renaissance Dam.