The meeting was attended by Egypt's intelligence chief Abbas Kamel.
Coinciding with the Sisi-Haftar meeting in the Egyptian capital, the UN's envoy to Libya said on Sunday that the body's position on ending the country's turmoil would "not change".
Since the overthrow and death of Muammar Gaddafi in 2011, Libya has been ruled by rival administrations in the east and west of the vast, oil-rich country.
Troops loyal to Libya's internationally recognised government have shot down a fighter jet belonging to the eastern forces under the command of Khalifa Haftar, on the same day the renegade general held talks with Egypt's president in Cairo.
Egypt and the United Arab Emirates publicly support U.N. -led peace efforts in Libya, while being seen as Haftar's closest regional allies.
It is not clear whether Haftar's surprise march on Tripoli was launched with the prior knowledge or the approval of the Egyptians.
The eastern-based army has been leading a military campaign against the government in the capital Tripoli since earlier this month, attempting to take over the city. Moreover, militias, mostly Islamist, have held sway over large regions, particularly in the west and south of the country.
At least 121 people have died in clashes between rival militias fighting for control of Libya's capital, the World Health Organization (WHO) said on Sunday.
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"Three medical personnel have been killed and five ambulances have been incapacitated by shrapnel", OCHA said in a Saturday statement.
The World Health Organisation tweeted that it "strongly condemns repeated attacks on health care workers, vehicles".
The sides in the civil war "which were fighting Daesh are now fighting each other", said Tarek Megerisi, a policy fellow with the North Africa and Middle East program at the European Council on Foreign Relations.
WHO's Libya Twitter account posted an update of "casualties" and said it was "sending medical supplies, health staff support for first- and second-line responders".
The U.N. Office for the Coordination of Humanitarian Affairs said more than 13,500 people have been displaced, and that "significant numbers of civilians" remain stuck in areas where the fighting has escalated.
"The humanitarian community repeats its warning that continuing to attack medical and civilian facilities is a violation of global humanitarian law and human rights law", OCHA said in a statement.
Bashagha told a United States-based Arabic language TV channel on Friday that they received information about an aircraft that came from UAE and landed in Benghazi's Benina Airport with military equipment for Haftar's forces in violation of the UN arms embargo.