The Egyptian diplomatic mission in the Yemeni capital Sanaa returned to Cairo on Monday due to the degrading security situation, state news agency MENA reported.
The Egyptian embassy in Sanaa shut down following the departure of the mission.
Yemen has been gripped by chaos since Shia Houthi rebels took control of the capital and challenged the central government. The poor Arabian Peninsula state is also fighting a local Al-Qaeda branch on its territories, one of the strongest offshoots of the group.
The situation worsened after the Western-backed Yemeni President Abedrabbo Mansour Hadi fled to Aden on Saturday after sneaking out of his residence in Sanaa, where he was being held by a Shiite militia group that has seized control of the capital.
Hadi said he is still the legitimate president and that he had resigned earlier only under pressure.
The Houthis last month seized the presidential palace and besieged Hadi's residence, prompting him to offer his resignation.
They have pushed their advance south and west into mainly Sunni areas of Yemen, where they have met with fierce resistance from tribesmen and Al-Qaeda.
The crisis has raised fears of Yemen – a key US ally in the fight against Al-Qaeda that borders Saudi Arabia – collapsing into a failed state.