The first of 180 expelled peacekeepers headed to Addis Ababa where they have been temporarily reassigned.
The withdrawal comes amid soaring tensions along the Ethiopian-Eritrean border and fears of a new war between the rival Horn of Africa neighbors.
"We are at a critical time," said Jean-Marie Guehenno, the head of UN peacekeeping operations, who had for three days unsuccessfully sought meetings in Asmara to press for the expulsion order to be reversed.
Eritrean officials refused to see him, a situation he called "unfortunate" shortly after the first of three flights bringing 87 peacekeepers to Ethiopia departed from Asmara.
Last flights
An Agence France Presse correspondent in Addis Ababa said later that the last of the three of flights landed at 6:00 p.m. local time (1500 GMT), as had four UNMEE helicopters previously based in Eritrea along with their crews.
In Asmara, Mr Guehenno said two more UNMEE staff would leave on Friday and that the remainder of those affected by the order were already out of Eritrea.
"The overall political situation is certainly not good," he told reporters.
"Never has there been such a great crisis for the mission."
"We really are at a crossroads," Mr Guehenno said, referring to the status of the UN Mission in Ethiopia and Eritrea (UNMEE) which is tasked with monitoring the border, as well as relations between the United Nations and Eritrea.
On Wednesday, the UN Security Council decided to withdraw the UNMEE's 180 Eritrea-based US, Canadian, European and Russian staff in line with the Asmara government’s order, along with another 20 personnel at the mission's headquarters here.
The council condemned the order as "unacceptable" and renewed demands that all restrictions imposed by Eritrea on UNMEE, including an October ban on helicopter flights, be said.
Mr Guehenno said the 15-member Security Council would make "critical decisions" about UNMEE in January after assessing the impact of the expulsions, which are believed to be the first ever directed at peacekeepers from specific nations.
"In my ten years as the head of peacekeeping, I have not been confronted with a similar situation," he said.
Eritrea angry
Diplomats say the expulsions are a sign of Eritrea's increasing anger at the failure of world powers to push Ethiopia to accept an international ruling on the border in 2002 that awarded the flashpoint town of Badme to Asmara.
Ethiopia and Eritrea fought a bloody 1998-2000 trench war over the border that claimed some 80,000 lives and the government in Asmara says new conflict is looming because authorities in Addis Ababa have rejected the binding border demarcation.
The expulsions are the latest in a series of restrictive measures Eritrea has imposed on the UNMEE, which has reported troop movements on both sides of the border and says the situation is "tense and potentially volatile."
In November, the Security Council threatened both Ethiopia and Eritrea with sanctions if they returned to war and did not pull troops back from the border.
It also warned Eritrea alone of sanctions unless the restrictions on the UNMEE were lifted, a position that the Asmara government angrily denounced, accusing the United Nations of ignoring Ethiopia's rejection of the border ruling.
Instead of easing those restrictions, Eritrea issued the expulsion order, prompting UN chief Kofi Annan to dispatch Mr Guehenno and military adviser Randir Kumar Mehta to the region in a bid to calm tensions.
After securing a pledge from Ethiopia to pull back recently deployed soldiers from the border, the envoys were snubbed by Eritrean officials who refused to acknowledge their presence in Asmara.
The UNMEE has 3,794 peacekeepers and support staff on both sides of the 1,000-kilometer border, many of whom are based in Eritrea and patrol a 25-kilometer buffer zone in Eritrean territory.