"We want you to keep going. We're very committed," Clinton said as she met Thein Sein, a former junta general chosen by parliament last year to lead a quasi-civilian government.
In the 15 months since taking power, Thein Sein has begun to liberalize Myanmar's economy, released more than 670 political prisoners, permitted greater media freedoms, legalized protests and undertaken peace talks with rebels.
Clinton and Thein Sein met at a business conference in Siem Reap, Cambodia, two days after the United States eased sanctions to allow US companies to invest in Myanmar and provide financial services in the country, also known by its British colonial name Burma.
Posing for pictures before their talks, Thein Sein said: "I am very pleased to see that our bilateral relationship (is) improving dramatically. And we are pleased that President Obama eased the sanctions."
"Today, after nearly half a century, Myanmar has embarked on a democratic path in building a new nation through peaceful transition. Myanmar is at a crucial juncture where she has evolved from a military administration ... and (is) moving toward a new democratic era while endeavouring (to work) for the development of the country," he said in a text prepared for delivery to the conference.
While creating exceptions to the sanctions, Obama has formally left them in place, retaining leverage over Myanmar if the government should start backsliding on reforms.
On Wednesday he required American companies to make detailed disclosures about their dealings in the hopes of increasing transparency in Myanmar, among the world's most corrupt countries according to watchdog Transparency International.
While the sanctions relief was a strong sign of support for Myanmar's reforms, Obama said their unfinished state left him "deeply concerned about the lack of transparency in Burma's investment environment and the military's role in the economy."
In a land of widespread poverty but rich in timber, gems and gas, Myanmar's crony capitalists - a clique of fewer than 20 families - grew rich with help from Than Shwe, a military dictator who ruled from 1992 until he stepped aside last year.
'Short period of time'
Clinton and Thein Sein met for about an hour, a senior US official told reporters, saying Clinton had voiced concern about reports that 10 staff members from the United Nations and other international organisations had been detained in Myanmar and charges had been lodged against some of them.
Speaking at the conference, Clinton praised Thein Sein as a leader "who has moved his country such a long distance in such a short period of time."
Without naming Myanmar, however, she also stressed the importance of democratic reforms and good business practices, saying these were vital for long-term growth.
"The difference between a region on the path to sustainable growth and one whose gains will be more short-term are the norms and the standards for intellectual property protection, for predictability in setting rules and enforcing laws to try to ensure a level playing field for everyone," she said.
Thein Sein said he was committed to reform, citing his efforts to liberalize the economy, permit protests and move toward a democratic system, but he complained of the continued imposition of foreign sanctions and of Myanmar's inability to receive funding from international financial institutions.
"With the establishment of a new government in Myanmar, the people of Myanmar wish to see true change in the country," Thein Sein said, speaking in English. — Reuters