Biden spoke to Al-Khalifa on Thursday and "emphasized the importance of reducing ongoing tensions through dialogue and reconciliation with the opposition, and a commitment to reform," the statement on Friday said.
Bahrain, which hosts the United States' Fifth Fleet drew US and United Nations criticism this month when it moved to strip a top Shiite cleric's citizenship and closed the main Shiite opposition group.
A US State Department report, first reported by Reuters, found Bahrain's national reconciliation efforts have stalled after it crushed street protests in 2011, and said the Western ally in the Persian Gulf has not implemented recommendations to protect freedom of expression.
Earlier this week, the State Department said Bahrain's plan to try an activist for tweets condemning its prison system and involvement in the war in Yemen is worrisome to the United States.