Military operations in Rakhine State have caused thousands to flee across the border to Bangladesh. A UN official said Rohingya in Burma were being ethnically cleansed with Rohingya alleging that government soldiers have killed and raped civilians.
The military action – launched in response to coordinated attacks by armed men on border posts in October - has left scores of people dead.
The army says it is fighting an armed insurgency in the region and the government denies abuses. “The international community misunderstood us because of Rohingya lobbyists who distributed fabricated news,” the presidential spokesman, Zaw Htay, said this week. “No one in the world would accept attacks on security forces, killings and looting of weapons.”
Ms Suu Kyi’s failure to speak out in support of the Rohingya "is baffling to an international audience that persists in casting her as a human rights icon", said David Mathieson of Human Rights Watch.
"One version to explain her silence is callous indifference, another is calculated limited messaging ... but the most likely is she simply has no control over the Burmese army," he added.
Researchers at Queen Mary University London said her silence amounts to “legitimising genocide” and entrenching “the persecution of the Rohingya minority”.
"Despite the fact that this is the most significant test of Suu Kyi's leadership, the country's de facto leader has remained remarkably indifferent," they said.
Rights groups say the military has used the attack on police border posts last month as an excuse for a crackdown on the Rohingya.
The Rohingya, a group of around a million, have been resident in Burma for decades – but are treated as illegal immigrants and denied citizenship.
Ms Suu Kyi took power this year after winning the country's first free elections in a generation. She stood on a platform of reconciliation for people across the country, but she has been hampered by a junta-era constitution that gives the army a quarter of parliamentary seats and control over security.
She also faces a prevailing view among many of Burma's Buddhists that the Rohingya are illegal immigrants and any move to support them would risk a public backlash.
Reports in Rakhine state cannot be independently verified because the government restricts access for journalists and aid workers. Aung San Suu Kyi has said a government-led investigation is under way.
Malaysia will summon Burma's ambassador over the crackdown on the Rohingya Muslims, it said on Friday, as protesters across South-east Asia demonstrated against the rising violence.
The Malaysian foreign ministry called on all parties involved to refrain from actions that could aggravate the situation.
"Malaysia also calls on the government of Myanmar [Burma] to take all the necessary actions to address the alleged ethnic cleansing in the northern Rakhine State," the ministry said in a statement.
"The ministry will summon the ambassador of Myanmar to convey the government of Malaysia's concern over this issue," it added, without giving a timeframe.
Hundreds of Rohingya Muslims marched in the Malaysian capital of Kuala Lumpur, condemning the bloody crackdown on the persecuted minority and criticising Nobel Peace Prize winner Ms Suu Kyi for her inaction on the matter.
Protesters demanded humanitarian aid for Rakhine, and urged that the military seize all attackers.
Protests were also held simultaneously in Bangkok, the capital of neighbouring Thailand, in Bangladesh and in the Indonesian capital of Jakarta.
Agencies contributed to this report.
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