India is still on edge after gunmen killed 166 people in a three-day rampage on the financial hub last November.
Hundreds of Muslims were detained and questioned over the attacks, angering rights activists who said innocent people were caught up in the backlash.
"The horrific terrorist attack in Mumbai has also polarized society and risks stoking suspicions against the Muslim community," said U.N Human Rights chief Navanethem Pillay.
"Both internal and external terrorist threats have led to counter-terrorist measures that put human rights at risk," Pillay said in New Delhi during her India visit.
Religious and caste-based prejudices remain entrenched in Indian society, she said.
Secular India has a long history of tensions between its majority Hindus and minority Muslims that have exploded in deadly violence. More than 2,000 people, mainly Muslims, were killed in communal riots in Gujarat state in 2002.
After the Mumbai attacks, the government rushed through new laws in December to allow police to hold suspects for up to 180 days without charge and created a new FBI-style national police force, in what was seen as an attempt to soothe public anger.