The trouble erupted on 25 August when Rohingya militants attacked security posts, triggering a military crackdown.
Newly arrived Rohingya Muslims from Myanmar prepare to leave a madrasa that they used as a transit shelter in Shahparirdwip, Bangladesh, Monday, Oct. 2, 2017.
"The two sides have agreed to a proposal to set up a joint working group to coordinate the repatriation process", Ali said.
They were divided into three groups and flown to Maungdaw and Rathedaung townships to meet with local people-Rakhine, Muslims, Mro and Hindu-from six villages in the areas.
The UN welcomed the trip but reiterated the need for greater humanitarian access.
"The scale of the human suffering is unimaginable and the United Nations sends its deepest condolences to all those affected", it said, calling for an end to the "cycle of violence".
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The foreign embassies encouraged the government to enable the "voluntary, dignified and safe" return of more than a half a million refugees in Bangladesh to their places of origin.
Bangladesh, which has accused Myanmar of committing genocide against the Rohingya and called on it to resolve the refugee crisis, has struggled to accommodate the influx of new refugees in existing camps in the country's southeast where another 400,000 Rohingya already live.
He gave no timeframe and did not say whether Myanmar would also take back 300,000 Rohingya refugees who fled across the border during earlier violence.
Ali said both countries agreed to form a joint working group to start work on the massive repatriation. Suu Kyi in a speech last month had said that Myanmar would take back only "verified" refugees.
"We are looking forward to a peaceful solution to the crisis", said the top Bangladeshi diplomat following the talks. Chris Lewa from the Arakan project, which closely tracks developments in Rakhine, said economic deprivation and tensions with Buddhist neighbours appear to be the main forces driving the recent movements of Rohingya out of Buthidaung, as opposed to fresh outbreaks of violence.