In a speech to the nation following the release last week of an official report into last year's violence in western Rakhine that killed around 200 people, Thein Sein said the country should aim for "peaceful coexistence".
"Regarding Rakhine, our government will take responsibility for upholding Muslims' fundamental rights," he said, adding that ethnic Rakhines, who are mainly Buddhist, "will not be neglected".
Rakhine state remains deeply divided following major eruptions of unrest in June and October that saw mobs rampage through villages and torch thousands of homes, displacing 140,000 mainly Rohingya Muslims.
Thein Sein said he accepted that "there were human rights violations... Because of the policies that we used formerly", without elaborating on which measures he was referring to.
He pledged to use his authority "to make sure that security forces fully implement measures to restore peace and the rule of law".
Attacks against Muslims -- who make up an estimated four percent of Myanmar's population -- have exposed deep fractures in the formerly junta-run country and cast a shadow over reforms under a quasi-civilian regime that took power two years ago.
A renewed bout of anti-Muslim unrest last week saw one killed and mosques and homes destroyed in Oakkan, around 100 kilometres north of Yangon, as the unrest spread closer to the country's main city.
The Rakhine commission called for increased aid in Rakhine, where tens of thousands of Rohingya are trapped in squalid camps amid fears of a deepening humanitarian crisis as the monsoon season approaches.
But the report also recommended maintaining the segregation of the two communities while tensions remain.
Rohingya -- considered by the United Nations to be one of the world's most persecuted minorities -- have been rendered effectively stateless in Myanmar with few rights and scant access to public services.
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