The diplomat took part in an official ceremony, during which he and 13 other nations' ambassadors submitted their letters.
Last month, Amitai was temporarily recalled
from Cairo due to concerns for his safety during the one-year anniversary to the Egyptian uprising.
Amitai, who has previously served as a diplomat Cairo, recently replaced former Ambassador to Egypt Yitzahk Levanon.
His previous roles include an ambassadorship to Ethiopia. He has also held a variety of research positions and is considered an expert on Arab affairs.
The Israeli-Egyptian ties have suffered setbacks in recent months, after a popular revolt unseated Egypt's then-President Hosni Mubarak.
In September, protesters angered by Israel's killing of Egyptian policemen on the border raided the Israeli embassy in Cairo, bringing to the evacuation of the mission's staff and their families.