But the International Organization for Migration (IOM) said the new arrivals - the majority of them women and children - are at risk of human trafficking, as officials and aid workers struggle to cope with the influx.
Myanmar's de facto leader Aung San Suu Kyi cancelled her trip to the United Nations General Assembly in NY, which begins next week, while criticism on her handling of the Rohingya crisis grows and her government has been accused of ethnic cleansing.
The violence in western Myanmar began on August 25 when Rohingya insurgents attacked about 30 police posts and an army camp, killing about 12 people.
Van Thio did not use the term Rohingya, referring to them simply as Muslims.
Myanmar's de facto leader and a Nobel laureate Suu Kyi has been slammed widely for her silence on what the United Nations described as a "textbook example of ethnic cleansing".
More than 420,000 have fled since Rohingya insurgent attacks on security forces last month prompted a crackdown.More news: Mueller's Russian Federation team reportedly seeks White House records on Trump actions
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Pence called the crisis a threat to the world and said US President Donald Trump wanted the UN Security Council to take "strong and swift action" to the violence.
Pence also spoke about how the violence in Myanmar is a ideal example of the kind of problem the United Nations should help solve.
Addressing the gathering at the National Human Rights Commission's (NHRC) two-day national seminar on good governance and human rights, Rajnath said, "The Rohingya Muslims are not refugees as they have not completed the legal process".
Much of the speech appeared meant to frame the crisis as a complex internal issue and contrasted the violence - which she depicted as isolated - with the government's ongoing development agenda, specifically its efforts to deliver "peace, stability, harmony and progress" to the nation as a whole.
He said a committee had been established under the social welfare minister to implement recommendations of an advisory commission chaired by former UN Secretary-General Kofi Annan and the government would establish an advisory board comprised of "eminent persons" from Myanmar and overseas.
Since Aug. 25, more than 421,000 Rohingya have crossed from Rakhine into Bangladesh, according to the UN.