In her first address to the UN General Assembly as national leader in September a year ago, Suu Kyi defended her government's efforts to resolve the crisis over treatment of the Muslim minority.
Meanwhile UN agencies UNHCR and IOM have launched a joint appeal seeking enhanced humanitarian assistance for fleeing Rohingyas fearing their number could exceed a million as surges of the minority ethnic community from Myanmar continued to hit Bangladesh.
Antonio Guterres said alleged attacks by security forces on Rohingya villagers were completely unacceptable.
But the authorities have denied that the security forces, or Buddhist civilians, have been setting the fires and have blamed the insurgents instead.
Next steps: The UN Security Council plans to meet Wednesday to discuss the crisis, according to BBC.
Suu Kyi has been repeatedly criticized over her response to the crisis.
Bangladesh's Foreign Minister Mahmood Ali on Sunday accused the Myanmar government of committing genocide against the Rohingya, who it does not recognise as an ethnic group.
Guterres said many women and children were arriving in Bangladesh "hungry and malnourished".
She was needed in Myanmar to "manage humanitarian assistance" and "security concerns" caused by the violence.
"Many of the Rohingya who flooded into refugee camps in Bangladesh told of Myanmar soldiers shooting indiscriminately, burning their homes and warning them to leave or die".
"The first reason [Suu Kyi can not attend] is because of the Rakhine terrorist attacks", the spokesman, Zaw Htay, said in a news conference, according to The Associated Press.
The country's de facto leader, Aung San Suu Kyi, has been criticised by fellow Nobel Peace-prize laureates, the Archbishop Emeritus of Cape Town, Dr Desmond Tutu, and Malala Yousafzai, for staying silent in the face of mounting evidence of persecution. "We have heard them saying, 'No Rohingya in Myanmar.' But we will go back", Arif said.
"One is the current situation in Rakhine state".
ACTION: Please ask the NewsHour to return to the Rohingya story with a report that treats the question of ethnic cleansing as more than a matter of opinion. "The state counsellor won't attend the meeting of the United Nations General Assembly", said government spokesman Zaw Htay, using Suu Kyi's formal title.
"The added challenge is that a lot of people are crossing the border, going to makeshift settlements, or otherwise living outside more organised structures, which could make it easier for us to reach them", he said.