UN Special Rapporteur Yanghee Lee said that Suu Kyi should "speak up a little more" to protect the Rohingya, tens of thousands of whom have fled across the border to neighboring Bangladesh in recent months.
Responding to Lee's comments, Myanmar government spokeswoman Aye Aye Soe said the administration was "deeply concerned by reports of potential human rights abuses and have already set up an investigation commission."
Unrest
The violence began on October 9, when according to state media, a group of around 300 armed men attacked soldiers and police, sparking an intense crackdown by the Myanmar military.
"We, the vulnerable and persecuted people, have asked the international community for protection against the atrocities by the government of Myanmar, but the international community turned its back on us," he said.
"Finally, we cannot take it anymore."
The Myanmar military has arrested hundreds of people in Rakhine, deployed attack helicopters and allegedly torched villages, causing thousands of refugees to flee the region.
Divisions
Suu Kyi was barred from becoming Myanmar's president after the country's transition to limited democracy in 2015, but as state counselor she is the country's de facto leader.
The longtime democracy campaigner and Nobel Peace Prize Laureate told the BBC the situation in Rakhine was more complicated than the international media had made it out to be.
"I think there is a lot of hostility there -- it is Muslims killing Muslims as well, if they think they are cooperating with the authorities," she said.
"It is not just a matter of ethnic cleansing, as you put it -- it is a matter of people on different sides of the divide, and this divide we are trying to close up."
She said she'd been pressed to answer questions about her stance on the Rohingya since 2012, when sectarian violence broke out.
"(Reporters) would ask me questions and I would answer them, and people would say I said nothing. Simply because I did not make the statements people wanted, which people wanted me to make, simply to condemn one community or the other," Suu Kyi said.
Military rule
While Suu Kyi is the most powerful civilian politician in Myanmar, the country's military still possesses a great deal of influence.
Under the constitution -- drafted by the former junta -- the military retains 25% of the seats in parliament, and control of security matters.
Suu Kyi denied this week that the military had free rein in the region.
"They are not free to rape, pillage and torture," she said. "They are free to go in and fight. That is in the constitution. Military matters are to be left to the army."
She promised that Rohingya who have fled Myanmar to neighboring countries "will be safe" if they returned.
"We welcome them and we will welcome them back," Suu Kyi said.
CNN's Bex Wright contributed reporting.