The pamphlets telling Jews to register or be expelled were distributed in the city of Donetsk and sparked global outrage and fears of a Nazi-style pogrom.
"The president expressed his disgust quite bluntly," said Obama's national security advisor Susan Rice.
"I think we all found word of those pamphlets to be utterly sickening, and they have no place in the 21st century."
Rice said that Secretary of State John Kerry, who condemned the leaflets on Thursday in Geneva, had made US objections clear to Russian Foreign Minister Sergei Lavrov.
The pamphlets carried the stamp of the pro-Russian insurgency and signature of one of its leaders.
The US embassy in Kiev first raised concerns over the leaflets, which it said appeared to be an attempt to stir fear.
The chief rabbi in Donetsk said that he saw the leaflets as "provocation".
They contained a demand for every Jew to gather at the seized local administration building on 3 May to pay a fee of $50 to register or face the threat of being expelled from the region.