Sunday's incident was "spontaneous" and the migrant workers involved were employed by a variety of companies and lived in different places, he told reporters in Tokyo on the sidelines of a summit.
Asked to comment on suggestions that a possible cause of the riot was pent-up tensions among foreign workers in Singapore, Lee said: "We have not seen any evidence of that. The riot happened spontaneously, it was localised.
"The people who were involved in the riot were not from one company, or one dorm; (they were from) several dorms, many different companies, and it is unlikely that all the companies will have the same problem."
Lee said there were some signs that alcohol was a factor, The Strait Times reported.
The trouble began after a bus fatally knocked down an Indian pedestrian, 33-year-old Sakthivel Kuaravelu, in Little India, a precinct of Indian-origin businesses, eateries and pubs frequented by most South Asian workers on Sunday.
Around 400 South Asian migrant workers were involved in the rampage that left 39 police and civil defence staff injured and 25 vehicles damaged. Thirty-three Indian nationals have so far been arrested and charged in court for alleged rioting.
Post riot, India assures support to its workers in Singapore
Two more Indians charged in Singapore for rioting
24 Indians charged for worst rioting in Singapore
24 Indians among 27 arrested in Singapore after riots
Three more Indians face rioting charges in Singapore