A total of 2,967 Egyptians crossed into Egypt through the Salloum border crossing which connects Egypt to its conflict-ridden neighbour Libya, a top security official told state news agency MENA.
Marsa Matrouh's Security Director al-Anani Hammouda said there are increasing numbers of Egyptians who are returning through the border crossing after the airstrikes launched by the Egyptian air forces.
Hammouda had declared a state of emergency at the Salloum crossing last week.
The evacuation of Egyptians from Libya comes after a video surfaced showing the beheadings of 20 Egyptian nationals and another man, who is not believed to be Egyptian.
In response, Egypt struck militant targets in Libya on Monday.
Earlier today, 192 Egyptians were flown home through Tunisia after crossing the Ras Jedir checkpoint on the Libyan-Tunisian borders.
The Egyptian community in Libya is estimated to be no less than 500,000, according to Foreign Ministry figures.
The unprecedented violence in the troubled neighbour has affected Egyptian nationals residing there since late 2013, with many Egyptians becoming the targets of attacks in Libya.
Egyptian authorities issued a ban on any travel to Libya a month ago.
This ongoing evacuation of Egyptians from Libya is the second in less than a year. Egypt's Aviation Ministry created an emergency airlift with Tunisia last July to transport Egyptians stranded on the Libyan borders with Tunisia back home.
