According to Antonio Guterres, the assaults were allegedly perpetrated by Myanmar's armed forces "at times acting in concert with local militias, in the course of military "clearance" operations in October 2016 and August 2017".
Myanmar says it has repatriated the first family of Rohingya refugees from Bangladesh, despite a United Nations warning that it is not safe to return.
"The widespread threat and use of sexual violence was integral to this strategy.as a calculated tool to force them to flee their homelands and prevent their return", Guterres said. The army has said its crackdown was provoked by the attacks of Rohingya militants on more than two dozen police posts and an army base last August.
Most Burmese consider the Rohingya as unwanted immigrants from Bangladesh, and the army refers to them as "Bengalis".
"Refugees in Bangladesh have said that before considering return to Myanmar, they would need to see concrete progress in relation to their legal status and citizenship, security, and their ability to enjoy basic rights at home in Rakhine State", the agency said.
Other countries include Syria, Iraq, the Democratic Republic of Congo, the Central African Republic, Sudan, South Sudan, Mali and Somalia.
"As a general trend, the rise or resurgence of conflict and violent extremism, with its ensuing proliferation of arms, mass displacement, and collapsed rule of law, triggers patterns of sexual violence", Guterres said.
Guterres said "ethnic cleansing in the guise of clearance operations unfolded in northern Rakhine state". And he said it remained "a heightened risk in transit, refugee and displacement settings". He said children born of this violence have been labelled "bad blood" or "children of the enemy" and warned that this vulnerability "may leave them susceptible to recruitment, radicalisation and trafficking".
On Saturday, just a day before Myanmar's announcement of the Rohingya family's arrival, the United Nations refugee agency warned that conditions in Myanmar were "not yet conducive for returns to be safe, dignified, and sustainable".
"Colombia is the only country in which children conceived through wartime rape are legally recognised as victims, though it has been hard for them to access redress without being stigmatised", he said.
Guterres reportedly lamented that "most incidents of mass rape continue to be met with mass impunity".
For example, Guterres said, not a single member of Islamic State extremist group or Boko Haram "has been prosecuted for sexual violence offences to date".