Speaking at a summit of Southeast Asian leaders in Bangkok -- with Myanmar's de facto head Suu Kyi in the room -- Antonio Guterres said he remains "deeply concerned" about the plight of the Rohingya.
Violence in Rakhine state in 2017 forced more than 740,000 Rohingya to flee, most seeking refuge in overcrowded camps in neighboring Bangladesh, in what UN investigators say amounted to genocide.
Myanmar does not recognize the Rohingya as citizens.
The country says it welcomes back those who agree to a bureaucratic status below full citizenship, and if they agree to live under tight guard after their villages were incinerated.
Guterres said Myanmar is responsible to "ensure a conducive environment for the safe, voluntary, dignified and sustainable repatriation of refugees".
Suu Kyi sat in the room expressionless as Guterres spoke, AFP reported.
Only a few hundred Rohingya have returned to Myanmar so far, with many fearing further persecution in the Buddhist-majority country.
The secretary-general also called on Myanmar "to ensure humanitarian actors have full and unfettered access to areas of return".
Despite repeated entreaties by the UN and endless criticism by rights groups and world leaders, Myanmar has refused to bend in its approach to the Rohingya.
Much of Rakhine remains largely closed to aid workers and journalists, who can only visit on tightly controlled, military-chaperoned trips.
It has launched an extensive and increasingly bloody campaign against Rakhine Buddhists, who are also fighting the central state for greater autonomy.
Suu Kyi has come under fire for failing to use her moral force to defend Rohingya after the 2017 unrest.
The treatment of the minority has shredded her image as an upholder of human rights in the eyes of the Western world.
Myanmar's army has come under fire for covering up the crackdown, which it blamed on Rohingya "terrorists".
A leaked ASEAN report earlier this year said the repatriation effort could take a further two years.
Suu Kyi has faced pressure over her country's treatment of the Rohingya from fellow ASEAN members Malaysia and Indonesia, which are both Muslim-majority.