The government had also said if allowed to stay, the Rohingya refugees would exhaust natural resources meant for Indians that could culminate in hostility towards them and lead to social tension and law and order problems.
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The hearing is taking place as Rohingya are facing severe violence in their native Myanmar.
The aid shipment was bound for the north of the Rakhine State where insurgent attacks on August 25 sparked a military backlash.
Myanmar's de-facto leader Aung San Suu Kyi said in a speech hours earlier that the country would take back verified refugees.
An official said the mob thought the aid was only for the Rohingya.
The predominantly Buddhist Myanmar considers them Bangladeshi, but Bangladesh says they're Burmese.
Meanwhile, pointing to a report issued by an advisory commission on Rakhine state headed by former United Nations Secretary General Kofi Annan, Suu Kyi said the Myanmar government will move forward with the verification process for refugees who have fled the country. A spokesman for the United Nations said the incident would further disrupt already extremely patchy aid delivery.
Rights groups accused the Myanmar military of burning Rohingya villages, raping women.
Myanmar considers the Rohingya illegal migrants from Bangladesh and refuses them citizenship, even though many have lived there for decades.
Van Thio said the government was concerned by reports that Muslims were continuing to cross into Bangladesh even though there had been no armed clashes since September 5 and added: "We would need to find out the reason for this exodus".
"Although Myanmar has undoubtedly made encouraging progress towards democracy in recent years, the situation in Rakhine, the appalling human rights abuses and violence are a stain on the country's reputation", British Foreign Minister Boris Johnson said.
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Myanmar denies that, saying its forces are waging a legitimate campaign against Muslim terrorists who have been attacking and torching villages of Buddhists and other non-Muslims, some 30,000 of whom were internally displaced. In reality, they sneaked-in through the Bangladesh border in southern Tripura and were planning to take a train to Guwahati and had plans to go to Delhi for getting refugee status card from UNHCR.