"I do not think we should depend on U.S. sanctions to keep up the momentum of our movement for democracy," she said. "We have got to work at it ourselves."
The U.S. Treasury Department, meanwhile, lifted sanctions Wednesday on Thein Sein and parliament member Thura Shwe Mann, allowing them do do business with Americans again.
Also Wednesday, Clinton compared Suu Kyi with another famous political prisoner.
She said she was reminded when she visited Suu Kyi during her house arrest that she saw similarities to Nelson Mandela.
"These two political prisoners were separated by great distances, but they were both marked by uncommon grace, generosity of spirit and unshakable will," Clinton said Wednesday. "And they both understood something we all have to grasp. The day they walked out of prison, the day the house arrest was ended, was not the end of the struggle. It was the beginning of a new phase."
Under Thein Sein, the Myanmar government has released hundreds of political prisoners in the past year, part of a series of reforms that have followed decades of repressive military rule. Western governments have responded to the efforts by starting to ease sanctions put in place to pressure the military regime.
Myanmar authorities have also engaged in peace talks with rebel ethnic groups and allowed Suu Kyi's party, the National League for Democracy, to successfully participate in special elections for the national parliament in April.
Suu Kyi and others have nonetheless cautioned that progress toward greater freedoms in Myanmar remains embryonic and fragile.
"I think one of the important reasons for her visit at this time is to remind us of how much more still lies ahead, from strengthening the rule of law in democratic institutions to addressing the challenges in many of the ethnic conflicts and in Rakhine state," Clinton said Tuesday in an introduction to Suu Kyi's address.
Communal violence between Buddhists and Muslims in the western Myanmar state of Rakhine this summer killed scores of people and displaced thousands of others. Human rights advocates have accused the authorities of cracking down particularly harshly on the Rohingya, a stateless ethnic Muslim minority, during the unrest.
Suu Kyi's U.S. trip coincides with a visit to New York by Thein Sein to attend the U.N. General Assembly, where he will meet with Clinton.
On Monday, the Myanmar government announced that it was releasing more than 500 prisoners as part of an amnesty. Suu Kyi said Tuesday that her party calculates that there were about 90 political prisoners among those released.
Between 200 and 400 political prisoners remain behind bars in Myanmar, according to different estimates.
Earlier this year, Suu Kyi visited Thailand, her first trip abroad since her release from house arrest, and then traveled to Europe, where she finally collected the Nobel Peace Prize she was awarded in 1991.
As part of her U.S. tour, she will visit Fort Wayne, Indiana, home to one of the United States' largest populations of Burmese expatriates. Since the early 1990s, about 5,000 Burmese have carved out a life there.
CNN's Ashley Fantz in Atlanta; and Jethro Mullen and Paul Armstrong in Hong Kong contributed to this report.
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