"The Ethiopian charge d'affaires was summoned in protest over the army-backed incursion in Sudan by Ethiopian militants who attacked Sudanese civilians and troops," the Sudanese ministry said in a statement.
A Sudanese military spokesman said Friday that a captain and several soldiers, as well as civilians, had been killed in clashes in the southeastern state of Al Qadarif.
The Foreign Ministry said there were children among the casualties. It added the Sudanese government would take measures to stop further incursions.
The state-run Sudanese news agency SUNA said Ethiopian villagers living in border areas frequently trespassed to Sudanese land to plant and harvest crops.