"This important step forward should continue the process of Iraqis taking responsibility for their future," Obama said in a statement after millions of Iraqis went to the polls to elect councils in 14 or Iraq's 18 provinces.
Security for the country's first ballot since 2005 was extremely tight with Iraqi police and military deployed in force, and Obama praised the technical assistance by the United Nations and other organizations to Iraq's electoral commission, which he said "performed professionally under difficult circumstances."
Obama said "it is important that the councils get seated, select new governors, and begin work on behalf of the Iraqi people who elected them."
Iraq, where US-led forces invaded in 2003 and ousted president Saddam Hussein, is struggling to emerge from years of sectarian strife and to strengthen its fledgling democracy.
Saturday's election is seen as a key test of Iraq's steadily improving security and political system as Obama seeks a withdrawal from the country in order to shift more troops to Afghanistan.
Last year Obama put forward a 16-month timetable for the withdrawal of US combat troops, but since taking office on January 20, when he said the United States would "begin to responsibly leave Iraq," he has not stated whether he would stick to such a timetable.
Obama, who opposed the Iraq war, has said he wants to redeploy thousands of combat troops from the country to Afghanistan, where conditions have deteriorated and which he says is the prime front against Al-Qaeda.