Egypt's army has set up two field hospitals on the border with Libya near the Salloum border-crossing town to receive returning Egyptians.
Libyan guards have withdrawn from their side of the boundary following anti-government protests, the army said on its Facebook page on Monday.
Hossam Zaki, Egypt's foreign ministry spokesman, said at least one million Egyptians reside in Libya where increasingly bloody battles between Libyan security forces and protesters have been taking place.
At least 100 buses carrying Egyptians are making their way to the Libya-Egyptian border, Zaki said.
Ahmed Aboul Gheit, Egypt's foreign minister, had also called on Libyan authorities to swiftly issue permits to allow planes to enter Libyan air space.
The foreign minister's request came after the Egypt made plans to send planes to Libya and collect more citizens once the situation stabilised.
Egypt rejected remarks made by Saif al-Islam Gaddafi saying Egyptians had a role in the events in Libya. Gaddafi's son had made the accusation "without any clear basis", state news agency reported.
Egypt held Libya responsible for the protection of Egyptian lives and property, it said.