"I should not have used the phrase 'walking time-bombs' to describe congregations of high density," she wrote in a Facebook post.
Phua is also the mayor of Central Singapore.
As her constituency covers part of the Little India neighbourhood, she had put forth some suggestions to safeguard against a repeat of the Little India riot in December 2013 -- involving South Asian workers -- the worst outbreak of public disorder in Singapore in 40 years.
During a recent visit to 'Little India', Phua said she noticed that the crowds that used to gather before the riot had returned, despite measures to ease large gatherings and alcohol sale restrictions in the area.
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Little India is a precinct of shops, hotels and motels where workers from South Asia spend their off days.
Her remarks triggered angry reactions.
"I have no intention to undermine any specific group," Phua explained.
"I personally get along very well with the foreign cleaners in my constituency. To them and the other foreign workers in our country, thank you for your help and please accept my sincere apology if I have caused you concern."