The award carries a citation and a cash prize of Rs two lakh, which is a new component introduced in the award from this year.
Singh was honoured for his work for the victims of Kandhamal violence in 2007-08.
Minority Affairs Minister K Rahman Khan, who was supposed to give away the award, could not attend the function with official sources maintaining that he was ill.
Singh told PTI that Odisha government had "appreciated" the award given to him and he was not aware if it had expressed any opposition.
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Singh, after receiving the award, said that the victims of Kandhamal violence are still awaiting rehabilitation.
"Most of the accused in 30 out 32 murders cases have been acquitted. So there is a feeling that justice is not being done to the victims. This award is a recognition of their struggle and the fact that they cannot be subjugated," Singh said.
The commission's chairperson Wajahat Habibullah said the annual event, which was not held last year, would go a long way in "mainstreaming the concerns of minorities".
"A large number of violations of their (minorities) rights are reported" and it was high time a parliamentary committee for them was constituted on the line of the Committee for the Welfare of SC & STs, Chatterjee said.
He also felt that the long-pending demand for an equal opportunity committee also needed to be looked into before any delay.