Prime Minister Meles is struggling to contain ethnic tensions
Melese Dayessa - a former minister in the regional government of Oromia - told the BBC he was facing persecution as a result of his ethnicity.
But the Ethiopian Government says Mr Dayessa has been spying for the armed separatist movement, the Oromo Liberation Front (OLF), and was dismissed from his position a month ago.
The defection is the latest sign of ethnic tension within Ethiopia's ruling coalition which is dominated by Prime Minister Meles Zenawi's Tigray People's Liberation Front.
Suspicious
Mr Dayessa fled last week through the town of Moyale, which lies on Ethiopia's border with Kenya.
Speaking on the BBC's Network Africa programme, he said he found it impossible to work and he felt unsafe.
The Oromo form the largest ethnic group in Ethiopia.
Mr Dayessa rejected allegations that he was collaborating with the OLF, which has been fighting for the independence of the Oromia region since 1973.
Mr Dayessa is accused of having "infiltrated" the government on behalf of the rebels.
"We have evidence that Melese Dayessa has been working for the OLF for a number of years and was involved in orchestrating student unrest," Suleyman Dedefo, an Oromia regional government spokesman, told the BBC.
Power struggle
In March, security forces in Oromia clashed for several days with students demanding aid for farmers. Five students died in the unrest.
Mr Dedefo said Mr Dayessa was dismissed from his ministerial post last month.
Last week he was also suspended from the Oromo People's Democratic Organisation (OPDO), one of the parties within the coalition government.
The controversy over Mr Dayessa comes less than a year after another senior Oromo politician, the speaker of Ethiopia's upper chamber, Almaz Meko, fled the country to the United States.
She accused the government of "bringing untold miseries and sufferings to the Oromo people".
Ms Meko's defection followed a power struggle within the ruling coalition, and the suspension of four Oromo officials for alleged corruption.