Speaking to journalists, Negeri Lencho, Minister of Ethiopia Government Communication Affairs Office (GCAO), said 98 suspects from Oromia regional state and five suspects from Somali regional state are under custody.
He further said the situation along the 1,500 km long common border of the two regional states has largely stabilized despite isolated flare-ups.
Heavy clashes along the Oromia-Somali boundary in September spilled into ethnic violence which left scores of people dead and tens of thousands displaced.
Oromia and Somali regional states have been locked in a dispute over the delineation of their common boundary for almost two decades.
A referendum in October 2004 was supposed to demarcate the boundary between the two regional states, but its implementation has been stalled ever since with both sides accusing each other of non-compliance.
The Ethiopian government has further pointed to competition to control illegal Khat trade as another reason for the conflict.
Khat, a mild stimulant leaf grown across Ethiopia, is chewed by millions of Ethiopians, who use it to help them conduct work, undertake home studies or use it for recreational purposes.
Oromia regional state is the largest Khat producing area in Ethiopia while Somali regional state borders Somalia and Djibouti, the main foreign destinations for Ethiopia's Khat exports.