On India's decision to deport Rohingya, Rajnath said, "Rohingya are not refugees, nor have they taken asylum".
"We are working heavily to help the refugees in Bangladesh", he said.
Myanmar was also working hard to enhance relations with Bangladesh and would welcome a visit by its home minister to discuss cooperation on border security, Van Thio said.
The UN human rights chief has described the systematic attacks against the Rohingya minority by the security forces as a "textbook example of ethnic cleansing".
The plight of the Rohingya, an Islamic minority in Buddhist-majority Myanmar, has evoked strong emotions across the Muslim world.
"It's important for them to understand that we are working in neutral and impartial way", she said, adding that the work is being done "with full transparency with the Myanmar authorities".
Pilot union BALPA urges Ryanair to improve working conditions
Separately, some Ryanair pilots have spoken to the BBC about a "toxic" atmosphere and how they felt "undervalued". As a result, the airline said it had to allocate annual leave to pilots in September and October.
Hundreds have been killed in violence since August 25, which has forced 420,000 Rohingya Muslims to flee army operations to Bangladesh.
In August, an advisory commission set up by Myanmar's government to find a solution to the crisis in Rakhine State - an entity chaired by former U.N. Secretary-General Kofi Annan at the request of Suu Kyi - made its final recommendations, including the introduction of a system for granting citizenship to the Rohingya. Tillerson "urged the Myanmar government and military to facilitate humanitarian aid for displaced people in the affected areas, and to address deeply troubling allegations of human rights abuses and violations".
Several hundred people tried to stop a boat being loaded with aid at a dock in the Rakhine State capital of Sittwe. "Provide security for them", she said on Tuesday at a reception by her Awami League's United States unit in NY where she is attending the UN General Assembly.
"The issue of national security is involved with regard to illegal immigration which our country can't undermine", he said.
After a series of attacks by Muslim militants last month, security forces and allied mobs retaliated by burning down thousands of homes in the enclaves of the predominantly Buddhist nation where the Rohingya live.
Nearly 40% of all Rohingya villages in Myanmar's Rakhine State are now empty, a government spokesperson confirmed earlier this week. Among other priorities, one of the primary themes of this year's General Assembly is bolstering support for humanitarian assistance to ongoing emergencies, in particular for refugees and the communities that host them.
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