India was not in competition for the seat since there were four countries and four seats for the Asia block. With 189 countries voting, Indonesia received 184 votes, Philippines 183, India 181 and Kuwait 166.
Other countries to be elected to the Council included Burkina Faso, Botswana, Congo, Benin, Czech Republic, Romania, Chile, Costa Rica, Peru, Italy and Austria.
These countries will begin their term on June 19 for a three year term.
In the wake of international condemnation of its crackdown on protesters, Syria gave up its seat to Kuwait.
UN Watch, a Geneva-based group that monitors the UN, said that Burkina Faso, India, Philippines and Indonesia had questionable qualifications to be on the human rights body.
It also said that Congo and Kuwait were unqualified to sit on the Council. UN Watch said that India`s statement on Syria`s recent crackdown had been "mixed."
It said that New Delhi had sent a "wrong message" to Damascus by not putting human rights first and giving credit to Syria for its "positive recent reforms."
India`s deputy envoy to the UN Manjeev Singh Puri dismissed the characterization that New Delhi did not have the qualifications.
Puri pointed out that India was the world`s largest democracy with most multi-ethnic and multi-cultural society.
Noting the votes received in the General Assembly, he told PTI, "This is the world`s affirmation."
Meenakshi Ganguly, the South Asia director of Human Rights Watch, said that India should play a positive and leadership role on the Council.
"Too often strategic interests or geo-political loyalties have come in the way of holding governments accountable for human rights violations and India should take the lead in altering this," she said.
In a letter sent to External Affairs Minister S M Krishna ahead of the Human Rights Council election, Amnesty International urged the Indian government to ratify the Convention against Torture Other Cruel, Inhuman or Degrading Treatment or Punishment.
On the domestic level, Amnesty International pointed out national human rights bodies lack independent initiative and adequate resources, and have a restricted mandate to deliver on key concerns within the country.
India is ranked as "Free" in the 2011 report published by the New York-based Freedom House, which an independent watchdog that supports the expansion of freedom.