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.
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.