Myanmar's Vice-President Henry Van Thio has said his government is "deeply concerned" about the exodus of people from Rakhine state into Bangladesh.
Speaking at the UN General Assembly, he said Myanmar was investigating "a problem of significant magnitude".
But he repeated the government line that the reason for the upheaval was unclear and that the "great majority" of Muslims had stayed behind.
De facto leader Aung San Suu Kyi has also downplayed the crisis this week.
She is facing rising criticism after she delivered a speech in Myanmar on Tuesday that did not address allegations of rampant rights abuses by the army against the mostly Muslim Rohingya minority in Rakhine.
She said more than half of Rakhine's Muslims - the Myanmar government does not use the term Rohingya - had stayed. She also claimed that there had been no acts of violence or village clearances since 5 September, which has been widely disputed.
On Wednesday Mr Van Thio repeated this view, saying: "I'm happy to inform you that the situation has improved."
He was speaking at the UN General Assembly in place of Aung San Suu Kyi.She declined to attend the General Assembly in order to handle the crisis.
He said not just Muslims but other minority groups had fled, and security forces had been told to "take full measures to avoid collateral damage and the harming of innocent civilians".
He also said aid would be distributed "without discrimination".
The Rohingya are denied citizenship in Myanmar and are widely despised.
More than 400,000 have fled from Rakhine to neighbouring Bangladesh amid a military crackdown, launched shortly after a 25 August attack on police posts by Rohingya militants.
The Burmese military is widely accused of committing atrocities amounting to ethnic cleansing.
The military says its operations are aimed at rooting out terrorists and has repeatedly denied targeting civilians.