Newly re-elected Obama, fresh from a historic jaunt to Myanmar, met Cambodian Prime Minister Hun Sen for talks in Phnom Penh ahead of joining an East Asia Summit.
"He began by expressing that his trip to Burma demonstrated the positive benefits that flow from countries moving down the path of political reform and increasing respect for human rights," said US deputy national security advisor Ben Rhodes, using Myanmar's former name.
Obama brought up the need for fair and free elections in Cambodia, and the need for the release of political prisoners, Rhodes added, agreeing that the meeting was "tense".
"He said that those types of issues are an impediment to the United States and Cambodia developing a deeper bilateral relationship."
Obama, the first US president to visit Cambodia, and Hun Sen shook hands before their meeting but the American did not smile during the greeting.
The Cambodian government has faced mounting criticism from rights groups in recent years for what they claim is a growing crackdown on dissidents and protesters in cases that are often linked to land disputes.
Dozens of Cambodian villagers faced with eviction staged several small protests ahead of Obama's arrival with "SOS" messages urging the president to help press the government on land rights issues.
During the talks, Rhodes said Obama highlighted the case of prominent government critic and radio station owner Mam Sonando, 71, who was jailed for 20 years in October for an alleged secessionist plot in a verdict that dismayed rights groups.
Hun Sen, 60, has been in power since 1985 and has vowed to rule until he's 90.
The country's main opposition leader, meanwhile, lives in self-imposed exile abroad to avoid jail term for what critics say are politically motivated charges.