It was midnight at a police barracks in the Indian state of Uttar Pradesh and in a freezing windowless room about 150 Muslim men and boys sat huddled, bloodied and bruised. Some of the shivering prisoners had raw gashes across their hands and faces, others had broken limbs splayed out at awkward angles. The beatings from police came frequently, according to multiple corresponding accounts; to those who asked for water or closed their eyes in drowsiness or simply did nothing at all. Over and over, metal rods and bamboo canes hit soft human skin. Some had been stripped of their clothes. The youngest among them was just 12 years old, said witnesses.

How hundreds of innocent Muslim residents of the city of Muzaffarnagar came to be rounded up on 20 December, before being tortured in police detention, is part of what Indian activist and academic Yogendra Yadav described as an unprecedented and ruthless “reign of terror” imposed upon the country’s most populous state over the past two weeks.

Since last month, India has been engulfed in the biggest nationwide protests in over four decades. People of all religions, classes, castes and ages took to the streets in opposition to a new citizenship amendment act (CAA) passed by the prime minister, Narendra Modi, and his Hindu nationalist BJP government, which many say discriminates against Muslims and undermines India’s secular foundations. The government has dealt with the dissent with increasing repression, with authorities banning gatherings of more than four people and demonstrators met with batons and tear gas.

Nowhere has the crackdown been so brutal and so openly communal against the Muslim communitythan in Uttar Pradesh. According to accounts given to the Guardian by dozens of victims, witnesses and activists, police in the state stand accused of a string of allegations: firing indiscriminately into crowds; beating Muslim bystanders in the streets; raiding and looting Muslim homes while shouting Islamophobic slurs and Hindu nationalist slogans; detaining and torturing Muslim children. The allegations further include forcing signed confessions and filing bogus criminal charges against thousands of Muslims who had never been to a protest.

Hundreds of Muslims and activists remain behind bars across Uttar Pradesh and thousands have been placed on police lists. And the orders, it appears, come from the very top.

BJP state chief minister, Yogi Adityanath, a militant Hindu nationalist notorious for his open hatred and persecution of Muslims, pledged to take revenge on protesters in the wake of the unrest. The police took him at his word. “It was kristallnacht for Muslims,” said activist Kavita Krishnan, describing the events that unfolded across the state on Friday 20 and Saturday 21 December.

That day in Muzaffarnagar, trouble began when a peaceful demonstration against the citizenship act turned violent as police clashed with protesters. Stones were pelted and vehicles were set alight. In response, police opened fire on the crowds. Nearby, maulana Asad Raza Hussaini, a respected Muslim cleric, and his students at Sadaat Madrasa, an Islamic seminary, were resting after afternoon prayers when about 50 police officers, bearing batons and iron rods, broke down the doors and burst in. They were allegedly looking for people who had taken part in the protest but upon entering the madrasa began violently smashing everything in their pathway.

Ruqaiya Parveen, 22, suffered a deep gash on her head, when police barged into her house in Muzaffarnagar, Uttar Pradesh, on 20 December, and beat up several members of the family. Photograph: Shaikh Azizur Rahman

“The maulana told the policemen gently that none from the seminary took part in any protest rally and pleaded for them not to vandalise the Qur’an centre in the madrasa,” said a neighbour who witnessed the police attack but did not want to be identified for fear of reprisal. “It was then that the policemen and Rapid Action Force personnel [a branch of the police that deals with crowd control] pounced on him.”

The police then rounded up Hussaini and 35 of his students, 15 of whom were under 18 and mostly orphans, and took them to a nearby police barracks. Here the cleric was, witnesses allege, stripped of his clothes, beaten and a rod shoved up his anus, causing rectal bleeding, while the students were allegedly tortured with bamboo rods and made to shout Hindu nationalist slogans Jai Shri Ram” [Hail Lord Ram] and “Har Har Mahadev” [Save us Lord Shiva].

“The maulana had been beaten up very badly and was left without a single cloth on his body and when he was released we found him in very bad shape,” said Salman Saeed, a local Congress leader who came to pick up Hussaini and several students from Civil Lines Barracks. “He was badly wounded and bloodied, with many bruises across his body. He could not stand up on his legs and was bare-bodied. We were shocked to see the maulana in that condition. He is bed-ridden now.”

While Hussaini and all his underage students were released at 2am that night, 12 adults students and the madrasa cook remain behind bars and have been charged with taking part in violence, despite never partaking in a protest.

The young students were not the only underage Muslim prisoners in Muzaffarnagar police barracks that night. Upon seeing the commotion in the streets, 14-year-old Mohammad Sadiq, who worked as a mason’s assistant, set out to find his 11-year-old brother. Cars and motorcycles had been set alight and as protesters were fleeing around him, he too began to run. It was then that a dozen police pounced on him, hitting his legs with batons to make him fall to the ground and then unleashing a torrent of blows, he said.

“The police said to me, ‘if you tell us the names of 100 Muslims involved in the riots we will stop beating you’,” recounted Sadiq, as he lay bed-bound and weak from his injuries in his one-room family shack. “I kept telling them I had nothing to do with the riots, that I did not know anything but they kept beating me. The policemen told me to shout ‘Jai Sri Ram’ and I told them I would not so they put an iron rod into the flames of the car that was on fire and then held it against my hands to burn me.”

“Then some of the police officers tried to pick me up and put me in the flames of the car on fire,” Sadiq said, “but two of them said ‘no, let’s just take him to the police station’.”

Sadiq was kept in police detention for the next four days. Stripped to his underwear, he said he was tortured. For two days he was given no food or water and no medical treatment for his badly bleeding wounds. When he was finally released his condition was so bad his mother, Rehana Begum, fainted when she came to collect him.

“His father is dead so he was the only earning member of this house but he has been beaten so badly across the knees he can not walk and can not work now so what will happen to us?” she said, her head in her hands.

Cars of a Muslim politician were set ablaze in

Muzaffarnagar on December 20. Photograph: Shaikh Azizur Rahman

According to multiple accounts, in the late-night raids on Muslim homes carried out in Muzaffarnagar and across the state over those two days, women, children and the elderly were not spared the brunt of the police brutality.

One such victim was 73-year-old Hamid Hasan, who was viciously beaten when police stormed into his house late on 20 December, using metal batons to attack him, his 65-year-old wife and his 22-year-old granddaughter, Ruqaiya Parveen, who was hit so hard across the head she collapsed from the wound and had to have 16 stitches.

Hasan wiped away tears as he showed the wrecked remnants of the wedding gifts purchased for his granddaughter’s forthcoming marriage, including a destroyed television, ripped sofa, overturned fridge and smashed air-conditioning unit he had saved up his whole life to buy. “My family did not take part in any protests, why would they do this to us,” wailed Hasan, who could barely walk from his injuries. “Muslims in this country are being made to live in fear, even in our homes we are not safe from violence now.”

Hasan’s 14-year-old grandson Mohammad Ahmad was also dragged from his bed by the officers, beaten in the street and then detained and allegedly tortured by police in the police barracks, along with Hasan’s son Mohammad Sajid, 40. Ahmad recounted how he witnessed officers force his uncle Sajid to sign a confession that a gun and bullets had been found in the police raid on their home. “He did not want to sign it but he had to because we were terrified,” whispered Ahmad softly, his legs still wrapped in bandages from the beatings.

After 24 hours Ahmad was released back to his family, but Sajid remains behind bars, his medical condition worsening by the day.

Official figures put the protest death toll in the state at 17. All were Muslim and the youngest was eight. Activists allege a deliberate obfuscation by the police around these deaths, with none of the families given postmortem reports.

The sole fatality in Muzaffarnagar on 20 December was Noor Mohammad, 26, a day-wage labourer who was shot over half a kilometre away from where the protests took place. Police allege he was killed by protesters. His wife, 23-year-old Sanno Begum, who is seven months pregnant with their second child, wept as she said all she wanted was “justice for my husband and my daughter”.

“If they are not giving us the postmortem report, then it must be the police who shot him. I want justice from the government. I have got a little daughter. I have no one to support us now,” she said through tears.

Not only did the police force the family to bury Noor 60km (40 miles) away from Muzaffarnagar, but they accompanied the body to the ground, prevented proper funeral rites being carried out and then confiscated the burial certificate from the family. “It is clear they want to destroy all evidence about his death,” said his brother-in-law Mohammad Salim.

The Muzaffarnagar police did not make themselves available for comment.

Over 500km across the state in the city of Kanpur, Mohammad Sharif, 74, sobbed as he described how his son Mohammad Raees, 30, died on 20 December in the crossfire of a protest. Raees had been working that day, washing utensils for a wedding, when he wandered out to see the commotion in the street and was hit by a police bullet. “He was not a protester, he was killed because he was Muslim,” said Sharif. “I want to die. Why I am alive when he is not? How can we go on living now?”

Almost two weeks have passed since the night of the raids but the climate of fear has not eased, with many abandoning their homes altogether. After the Guardian met with two activists in Kanpur this week, they were called into the police station and threatened with being charged with sedition if they spoke to the media again. They subsequently requested their identities be kept anonymous.

The Uttar Pradesh government insist its actions were justified. “Every rioter is thinking they made a big mistake by challenging Yogi ji’s government after seeing strict actions taken by it against rioters,” said the chief minister’s office in a recent series of twitter posts. “Every rioter is shocked. Every demonstrator is stunned. Everyone has been silenced.”

Shaikh Azizur Rahman contributed to this report