It said it had so far flown out 275 Ethiopians, some of whom had gun-shot wounds.
Yemen has been hit by months of instability, caused by the president’s refusal to bow to opposition demands to quit.
Two Somali migrants were killed in the capital, Sanaa, last month.
Yemen has long been a major transit point for illegal migration from the Horn of Africa.
The IOM said human traffickers were exploiting the instability in Yemen, bringing more migrants from Ethiopia and Somalia to Yemen.
The UN estimates that 37,000 Ethiopians and Somalis have been brought to Yemen so far this year.
They hoped to travel to countries such as Saudi Arabia, but many have been stranded at a camp on the Yemen side of the border.
An evacuated Ethiopian, who wanted to be identified only by his first name, Edris, told the BBC he had been traumatised by his experiences at the hands of the traffickers.
“I escaped from the centre where the traffickers had gathered us all, controlling and abusing women,” he told the BBC’s Focus on Africa programme.
“I saw women being raped by up to eight men. Even men were not spared from rape.”
The IOM said of the 275 Ethiopians it had evacuated, 34 were women and 115 were children.
It said it intended to evacuate another 1,900 Ethiopians stranded on the Yemen-Saudi Arabia border.
Analysts say Yemen is on the brink of a civil war as rival political, ethnic and religious groups fight for power.
President Ali Abdullah Saleh was wounded in a mortar attack on his compound in Sanaa earlier this month.
He was rushed to Saudi Arabia for treatment, and has not returned to Yemen.
He has been in power for more than 30 years, insisting that he will not yield to opposition demands to resign.
The US also fears that al-Qaeda is exploiting the political vacuum in Yemen to strengthen its influence in the country.