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Carrying placards saying "Not in my name", the protesters decried the silence of the Hindu nationalist government in response to public lynchings and attacks on at least a dozen Muslim men and boys since it took power in 2014.
In New Delhi, thousands of people, including the elderly and parents with young children, sang songs and lit candles.
In Mumbai, hundreds, including some Bollywood actors, gathered under umbrellas in pouring rain.
Protests were also reported in several other cities.
Last Friday, about 20 men attacked four Muslims on a train in the outskirts of New Delhi, fatally stabbing a teenager and seriously injuring two others.
The Muslim men said an argument over seats quickly turned into a brutal attack, with the mob accusing them of being "beef-eaters". Many members of the Hindu majority consider cows sacred. The slaughter of cows and eating of beef is illegal or restricted across much of India.
Much of the recent violence has been focused on cows. Several fringe Hindu groups, apparently emboldened by the stunning political rise of Prime Minister Narendra Modi's Bharatiya Janata Party, have attacked Muslim cattle traders and dairy farmers.
Muslims constitute about 14 per cent of India's 1.3 billion people, while Hindus comprise 80 per cent.
Rights groups say government officials, including the prime minister, have been slow to strongly condemn the attacks and that police action against perpetrators has been inadequate.
Five of the killings, almost all of them in broad daylight and in busy public areas, have taken place in the last three months.
On April 1, Pehlu Khan, a Muslim cattle trader, was lynched by a mob in the western state of Rajasthan as he transported cattle he had bought at an animal fair back to his home state of Haryana. Khan and his family were small dairy farmers.
In May, two Muslim men were beaten to death over allegations of cattle theft in India's northeast.
Over the last two years, vigilante groups, who call themselves cow protectors, have become active in small towns and cities across India. Even lower-caste Hindus who carry out undesirable tasks such as skinning dead cattle have faced mob violence.
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