Obama said he expressed concern about violence against Muslims in the country. "The displacement of people, the violence directed toward them needs to stop," he said.
Obama said they discussed Thein Sein's intention to release more political prisoners, institutionalise political reform and rule of law so it endures and work to end ethnic conflict. "As President (Thein) Sein is the first to admit, this is a long journey and there is still much work to be done," he said.
Thein Sein previously served in a repressive junta, and his meetings at the White House and Congress would have been all-but-impossible before he took the helm of a nominally civilian government in 2011. His name was only deleted from a blacklist barring travel to the US last September.
Six months ago Obama became the first sitting US president to visit the country also known as Burma. The administration's outreach to Myanmar's generals has provided an important incentive for the military to loosen controls on citizens and reduce dependence on China.
Myanmar has been rewarded by relaxation of tough economic sanctions, and Thein Sein will be addressing American businessmen keen to capitalize on the opening of one of Asia's few untapped markets.
The US last month announced it is considering duty-free access for Myanmar to US markets, and on Tuesday the two governments will sign a bilateral trade and investment framework agreement.
Obama repeatedly referred to the nation as Myanmar, a departure from the common US government reference to the country as Burma. White House spokesman Jay Carney said the US government has begun to allow limited use of the name Myanmar as "a diplomatic courtesy" to show respect for the ambitious reforms the country is pursuing.
The last visit by a Myanmar leader to the White House was in September 1966 by Ne Win, an independence hero-turned dictator, who began the nation's descent from regional rice bowl to economic basket case.
Human rights activists and Myanmar campaigners have sharply criticized the administration for inviting Thein Sein, arguing it sends the wrong message and wastes leverage to press for further democratic change. The administration says it is important to signal US support for his reform agenda, likely still opposed by military hardliners.
In his speech, Thein Sein said there may be "spoilers" who oppose reforms because their interests are threatened. He did not identify who the spoilers are, but drew a connection with the recent communal violence. He said the military has an "important role" to play in the process of democratisation and peace-building and was undergoing reforms.
Thein Sein expressed confidence of soon reaching a cease-fire with Kachin rebels. It is the only major ethnic insurgency that has yet to reach such a pact with the government, and fighting has escalated in the past two years, displacing about 80,000 villagers. He said this would require devolution of power and new agreements on resource-sharing.
"Our goal cannot be less than sustainable peace," the Myanmar leader said at the John Hopkins University School of Advanced International Studies.
Outside the White House on Monday, about 30 activists opposing Thein Sein's visit protested corruption in the government and treatment of ethnic Kachins. "We need real changes in Burma to stop the violations," said an organiser of the rally, Ye Htut of the International Foundation for Burma National Congress.
Despite the historic changes in Myanmar since 2011, Thein Sein's government has had a mixed record on reforms in recent months. It has freed more than 850 political prisoners in the past two years - including 19 before his Washington trip - but right groups say at least 160 are still held. The government has allowed Red Cross access to its prisons for the first time in seven years, but only limited humanitarian access to conflict zones, including Kachin State.
The US State Department on Monday again designated Myanmar as a country of special concern for its severe violations of religious freedom, as it has since 1999 in an annual global assessment. It said the government promoted Buddhism, practiced by the majority, over minority faiths that include Islam.
The department said there were credible allegations of the involvement of local border security authorities in the burning of villages during the communal violence in western Rakhine State, and of Muslims being arbitrarily detained since June, and reportedly denied food, water, and sleep. Some deaths in custody were reported, the department said.
- AP