At a hearing last month, The Committee on the Rights of the Child - an independent arm of the UN - urged the Hong Kong government to end the policy.
The hearing was held so the UN committee could review whether Hong Kong was sticking to the Convention on the Rights of the Child.
Those schools were once labelled as "designated schools" by the government. The tag was removed this year.
Hong Kong Unison director Fermi Wong Wai-fun, who campaigns for the rights of ethnic minorities, said: "It is a very strong tone for the report to confirm the existence of de facto discrimination."
The government hit back, saying the parents choose to put their children in the 31 schools. But the UN committee said the mainstream schools lacked the support to look after those students.
A spokesman for a designated school said a few months ago that to have ethnic minority students blend with students in mainstream schools would take a long time, as schools would have to be ready for the change. The current method allows designated schools to focus resources on ethnic minority students.
Equal Opportunities Commissioner Dr York Chow Yat-ngok said last month he would launch an inquiry into the city's education policy.
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