Myanmar's government imposed curfews and states of emergency last month in response to fighting between Buddhists and Muslims.
Myanmar President Thein Sein blamed "political opportunists and religious extremists" for violence between Buddhists and the Muslim minority in the country. The violence has claimed at least 40 lives since March 20.
Carter said during a visit to the country that he was concerned about an emerging culture of discrimination in the county.
"I am deeply concerned about the recent religious violence and tensions," he was quoted by Thai newspaper The Irrawaddy as saying. "I am also disturbed by frequent reports I heard since I've been here about hate speech."
Myanmar earned recognition for political reforms that began with general elections in 2010. Rights groups said the lingering violence may undo most of that progress, however.
"The recent violence risks damaging the reputation that you have gained for your country just as you are trying to rebuild it," warned Carter.