On a visit to Paris, Sein told France 24 television that his government was not guilty of the charges.
"Outside elements are just exaggerating, fabricating news, there is no ethnic cleansing whatsoever," he said.
"This is a smear campaign against the government. What happened in Rakhine was not ethnic cleansing."
In April, Human Rights Watch accused Myanmar of "a campaign of ethnic cleansing" against the Rohingya.
It cited evidence of mass graves and forced displacement affecting tens of thousands.
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Communal unrest last year in Rakhine left about 200 people dead and up to 140,000 displaced, mainly Rohingyas, who are denied citizenship by Myanmar.
Dozens more people died in Buddhist-Muslim clashes in central Myanmar in March.
Thein Sein, on a European tour that took him to Britain and France, said the unrest had been contained and insisted authorities were looking to prevent further violence.
"My government has set up an independent commission to investigate the root causes of this communal violence. We have also been implementing the recommendations issued by the commission.