The region’s president Abdi Mohamoud Omar, commonly known as Abdi Valley, was forced to resign on Monday and replaced by his finance minister Mr Ahmed Abdi Mohammed.
According to state-owned ESTV website, Mr Abdi was arrested and flown to the capital Addis Ababa on Tuesday.
“Officials from the Somali region in Ethiopia have confirmed to us reports of the arrest of Abdi Mohamoud Omar,” ESTV reported.
Mr Abdi was seen arriving at the Bole International Airport aboard a yellow military helicopter. He was not handcuffed.
Following uprisings in the region, the army and the federal police were ordered to enter the region to maintain peace at the invitation of the Somali Regional Council, the government said.
The deployment led to the standoff between the federal forces and the region’s paramilitary Liyu police and sparked protests by residents in the regional capital Jigjiga and Dire Dawa. It is reported that dozens of people died.
The property was also looted including banks and businesses as well as targeted killings of non-Somalis, according to AFP.
The Patriarch of the Ethiopian Orthodox Tewahedo Church, Abune Mathias, told state-affiliated Fana Broadcasting that seven churches were set ablaze and priests killed in the attacks.
“Prime Minister Abiy Ahmed deplores the violence and destruction of property in Jigjiga and Dire Dawa. He expresses his condolences for the tragic loss of lives. These tragedies and cycle of violence must end,” Mr Fitsum Arega, chief of staff of the Prime Minister said Monday.
Ethiopia is divided between ethnically demarcated federal regions that are intended to give different ethnicities a degree of self-rule but have been criticised for exacerbating ethnic tensions.
The Somali region, also known as Ogaden, is the second-largest and has been bedevilled by conflict lasting two decades with the government fighting the rebel Ogaden National Liberation Front (ONLF) that is seeking secession of the oil-rich region.
Ethiopia discovered an estimated 4.7 trillion cubic feet of gas and about 13.6 million barrels of associated liquids at the Jeexdin and Elale gas fields in the Ogaden Basin about four decades ago. The country, however, is yet to begin exploiting these resources due to communal conflicts and lack of infrastructure.
In June, the country began test-production undertaken by Chinese oil and gas exploration company Poly-GCL Petroleum Holdings Investment Ltd that saw three wells at the Ogaden basin generate 150 barrels of crude oil.
Rashid Abdi, Horn of Africa director at the International Crisis Group (ICG) think tank in Nairobi, said on Twitter that Prime Minister Abiy’s predecessors had relied on the regional president to pacify the Somali region and keep Islamist Al-Shabaab militants in neighbouring Somalia from entering Ethiopia.
But since taking office, Abiy has announced major reforms that Somali regional authorities believe would disrupt their hold on power, Mr Abdi said.
“They distrusted his reform agenda, concluded he was intent on disrupting the cosy arrangement that allowed the (Somali region) leader untrammelled power,” he said.
Rights groups have repeatedly accused the Somali regional government led by president Abdi Iley of committing rights abuses.
Last month, Human Rights Watch said regional authorities ran a secret jail where suspected members of a separatist group are tortured, raped and starved.