Guterres told the BBC on Saturday night that Suu Kyi had a last chance to stop the offensive.
“If she does not reverse the situation now, then I think the tragedy will be absolutely horrible, and unfortunately then I don’t see how this can be reversed in the future.”
The Secretary General reiterated that the Rohingya should be allowed to return home.
He also said it was clear that Myanmar’s military “still have the upper hand” in the country, putting pressure “to do what is being done on the ground” in Rakhine state where the crisis broke out on August 25 when Rohingya rebels attacked police checkposts and killed 12 security personnel.
Suu Kyi, a Nobel Peace Prize laureate, is facing growing criticism over the Rohingya issue.
She will not be attending the UN General Assembly in New York which will begin from Monday and has claimed that the crisis was being distorted by a “huge iceberg of misinformation”.
She said tensions were being fanned by fake news promoting the interests of terrorists.
Guterres’ warning comes after Bangladesh said it was now limiting the movement of more than 400,000 Rohingya who have fled from Myanmar.
The Rohingya, a stateless mostly Muslim minority in Buddhist-majority Rakhine, have long experienced persecution in Myanmar, which says they are illegal immigrants.