The mission, which includes five diplomats and six administrators, was recalled to Egypt after its chief envoy Ihab al-Sherif was slain by fighters. Al-Sherif was abducted in western Baghdad on 2 July.
A week after al-Sherif's disappearance, al-Qaida claimed on an Islamic web site that it had killed him to punish Egypt for supporting the US-backed Iraqi government.
Arab diplomats said the members of the mission had arrived in the Jordanian capital of Amman and would return to Egypt on Sunday. Egyptian embassy officials in Jordan declined to comment.
Last week, Pakistan's ambassador to Iraq, Mohammed Younis Khan, arrived in Jordan a day after escaping an attack by fighters seeking to discourage Islamic countries from bolstering ties with the Iraqi government.
Bahrain's ambassador to Iraq, too, was fired on in Baghdad last week.He was shot in the arm and evacuated to an Amman hospital for further treatment.