"Virtual demarcation is a legal nonsense," Wahade Belay, Ethiopia's foreign ministry spokesman, said on Thursday.
"It is invalid and unacceptable ... No border demarcation is recognised unless the lines are drawn on the ground and pillars are posted based on the agreement of both Ethiopia and Eritrea."
On Wednesday, Eritrea said it accepted the ruling and called on Ethiopia to remove its troops from Eritrean soil.
"Now after five years of revolving around the basic problem, the matter has finally been resolved through a virtual demarcation of the border," a statement published in the English-language Eritrea Profile newspaper said.
Thousands of troops face each other along the disputed border.
In the statement, Eritrea said it would pursue legal measures to evict Ethiopian soldiers from territory awarded to Asmara by the 2002 ruling.
"However, if legal proceedings do not result in the appropriate outcome, then the Eritrean people have other internationally approved choices," the government-owned paper stated, without describing what those options were.
Analysts and diplomats fear an incident along the frontier could spiral out of control and provoke a full-scale war.