Hailemariam Desalegn is serving as acting prime minister following the death of long-time Prime Minister Meles Zenawi this week.
The White House, in a statement, noted that Obama spoke with Desalegn, saying Meles was remembered for his contributions to peace and security in West Africa.
A former rebel fighter, Meles took power in 1991 after toppling the dictatorship of Mengistu Haile Mariam. He was credited with steering the country toward a role as regional power-broker.
Meles' ruling party, however, was accused of using repressive tactics to quiet his opponents after making sweeping democratic pledges, the International Crisis Group said this week.
The ICG reported that should conflict grow out of the power vacuum, it could spill across the Ethiopian borders.
Obama, the White House said, called on the acting prime minister "to use his leadership to enhance the Ethiopian government's support for development, democracy, human rights and regional security."
The former deputy prime minister serves in an interim capacity until 2015 elections.