"Peace and harmony are central to (India's) ethos. I appeal to my sisters and brothers of Delhi to maintain peace and brotherhood at all times," Modi said.
Yet the violence was itself sparked when supporters of the Citizenship Amendment Act (CAA), introduced by Modi's Hindu nationalist government, began to attack demonstrators in the Indian capital who had been peacefully protesting the bill on Sunday.
Modi's law fast-tracks naturalisation of foreign-born religious minorities of all faiths in South Asia except Islam.
The violence escalated on Tuesday and centred around Muslim-majority neighbourhoods - such as Maujpur, Mustafabad, Jaffrabad and Shiv Vihar - in north-east Delhi.
Read more: India's police 'watch in silence' as Hindu mobs attack Muslims, loot businesses and desecrate mosques
Hindu mobs armed with iron rods, bricks and bamboo sticks attacked the homes of Muslims in Mustafabad, while chanting "Jai Shri Ram," or "Victory to Lord Ram," the popular Hindu god of the religious epic "Ramayana", according to eyewitnesses who spoke to AFP.
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A man who fled his house with his family and took refuge in another mosque, now guarded by thousands of Muslims, spoke to AFP:
"I don't know if our house was burned or not, but when we were running away we heard them asking people to pour kerosene and burn everything down," Khan said.
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Among them was Mohammad Sameer, 17, who was being treated for a gunshot wound to his chest, sustained as he stood on his family's apartment terrace, watching Hindu mobs enter his district.
"When Sameer was shot, I took him on my shoulders and ran downstairs," said the boy's father, Mohammad Akram.
"But when the mob saw us, they beat me and my injured son. He was bleeding very badly."
They were stopped several times as they attempted to make their way to hospital, when mobs demanded that they pull their pants down to show whether they were circumcised.
Muslims are generally circumcised, while Hindus are not.
In Kardampura, a Muslim-majority area where a youth was shot and killed on Monday, hundreds of police personnel in riot gear patrolled the area on Wednesday and asked people to stay indoors.
"We are scared and don't know where to go," said one resident, Dr. Jeevan Ali Khan. "If the government wanted, they could have stopped these riots."
A resident of an area ravaged by anti-Muslim violence described making "many calls to the police" when mobs entered their area.
"But police did not help us at all. We tried to save the women at the protest site but instead policemen started beating us up," Naeem Malik said, showing wounds on his leg and hands.
When asked about the attacks at a news conference Tuesday, Donald Trump said he had not discussed the issue with his Indian counterpart and that it was "up to India."
"If we look back and look at what's going relative to other places especially, they have really worked hard on religious freedom," Mr. Trump said.
Sonia Gandhi, president of the opposition Congress party, accused Modi's nationalist party on Wednesday of giving "inflammatory speeches spreading an atmosphere of hatred and fear", including in Delhi city elections this month.
Congress "appeals to the people to reject the politics of hate", Gandhi said, calling Home Minister Amit Shah, Modi's close ally, "responsible" for the riots.
The violence has drawn sharp reactions from US lawmakers, with Rep. Rashida Talib, a Democrat from Michigan, tweeting, "This week, Trump visited India but the real story should be the communal violence targeting Muslims in Delhi right now."
Pakistani Prime Minister Imran Khan condemned the killing of Muslims, saying: "Now 200 million Muslims in India are being targeted. The world community must act now."
Since winning a second term, Modi's government has revoked the partial autonomy of Kashmir, India's only Muslim-majority state.
Together with the citizenship law, this has raised fears that Modi's broader vision is to remould India as a Hindu nation, something he denies.
Modi, 69, was accused of doing nothing to stop religious riots in 2002 when he was chief minister of Gujarat when around 1,000 people died, mostly Muslims.
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