This comes after they accepted the resignation of the outgoing President, Mulatu Teshome.
The attacker was also shot dead, he said.
Ethiopians and Eritreans have been celebrating the reopening of two key crossing points more than 20 years after a border war shut them.
The dead include 15 soldiers and three civilians, local reports say.
It’s believed that he has been pressured by the federal government to step down following protests and fighting between Somali and Oromo communities.
The prospects for the Horn could be transformed if the Ethiopia-Eritrea rapprochement holds and their border dispute is truly resolved.
The new leader's reformist agenda appears to have won some over.
The church which was often associated with the country’s ruling elites for centuries has a large following in Ethiopia.