Washington's top diplomat told President U Thein Sein on August 9 that while the United States acknowledged sweeping changes in Myanmar, fears remained over press freedom and religious unrest.
"We have seen remarkable progress over the past few years, but there is a long way to go," said a State Department official, adding that the US urged Myanmar to take actions to show that reforms were not "slowing down or regressing".
Kerry, who met U Thein Sein on the sidelines of regional security talks in Nay Pyi Taw, said it was "impossible not to be impressed" by the former pariah nation's reforms since 2011, which have seen most Western sanctions scrapped.
"As Myanmar tackles the challenges ahead I want the people of Myanmar to know that they have the support and the friendship of the United States," he said, ahead of a meeting with members of the Association of Southeast Asian Nations.
U Thein Sein, a former general who shed his military uniform to lead a quasi-civilian government three years ago, has been praised for broad reforms, including freeing political prisoners, scrapping draconian press censorship and welcoming opposition leader Daw Aung San Suu Kyi into parliament.
But a second State Department official said the country was facing more complex issues as it heads towards crucial 2015 elections that are likely to be won by Daw Aung San Suu Kyi's opposition National League for Democracy.
"They are now facing some (of) the deepest challenges -- what it means to change the governance structure of the country. And that has produced predictably some resistance, some slowdown," the official said.
In "candid" discussions, Kerry raised specific concerns over recent journalist arrests, religious violence and the severe health crisis in Rakhine State caused by chronic disruption to humanitarian access.
Deadly clashes in Rakhine two years ago have left some 140,000 people, mainly Rohingya Muslims, trapped in miserable displacement camps with scant access to basic services and work.
Communal violence has since erupted sporadically throughout the country, most recently in Mandalay, Myanmar's second largest city.
"One thing we are trying to explain to them is that time is not on their side, it is a less stable situation now on the ground that it was two years ago," the first official said.