About 450 people arrived in Israel on the last two planes chartered by Operation Dove's Wings, The Times of Israel reported.
The Ethiopian Jewish community, known as the Falash Mura, converted to Christianity in the 19th century to escape persecution but remained a distinct community. Thirty years ago, the Jewish Agency was given the responsibility of preparing those given permission to move to Israel for life there.
While about 7,500 made their way to Israel, about 12,000 Falash Mura were not given permission to immigrate and remain in Ethiopia, officials said. Members of the community in Israel have called on Prime Minister Binyamin Netanyahu to allow them to come to Israel.
Before the planes landed at Ben Gurion International Airport, hundreds of Ethiopian Israelis demonstrated outside Netanyahu's office.
Dov Lipman, a U.S. emigrant who sits in the Knesset (the Israeli Parliament) representing the centrist Yesh Atid Party, said he visited Gondar, Ethiopia, last year, and talked to Ethiopian Jews denied permission to enter Israel.
"I welcome the new immigrants arriving today," he said Wednesday. "However, there are hundreds, if not thousands, of daughters, sons, mothers, fathers, brothers and sisters of Ethiopians who are already in Israel who are being left behind. And we won't leave them behind."