Bashir is facing the most sustained challenge since he came to power in a coup in 1989. Demonstrators have turned out almost daily across the country to call for an end to his rule.
Bashir's trip to neighbouring Egypt is his second foreign visit since unrest began on Dec. 19. He has also visited Qatar.
Speaking next to his Egyptian counterpart Abdel Fattah al-Sisi, Bashir blamed unidentified "harmful organisations" for working to destabilise the region.
"We do not claim there is no problem, but it is not of the size or dimensions that some of the media portray."
"This is an attempt to copy the Arab Spring in Sudan, these are the same slogans and appeals and the very wide use of social media sites."
Citing what he said was the "harmful agitation" that countries affected by the Arab Spring witnessed, he added: "The Sudanese people are alert and will not allow for any intrusion or attempt to destabilise the security of Sudan."
Security forces fired tear gas cannisters at protesters gathered in at least four of the sit-ins, while in others demonstraters tried to block side streets leading to the main squares with rocks and other materials.
One of the slogans used by Sudanese protesters - "The people want the fall of the regime" - was made famous by uprisings in Tunisia, Egypt and other Arab states.
Sudanese security forces have deployed tear gas, stun grenades and live ammunition to disperse protests, as well as arresting hundreds of people.
Authorities say at least 30 people have died in the unrest while rights groups and local opposition figures say at least 45 have been killed.
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