Nationwide curfews are currently in place until Thursday morning and the army has warned of punishment for anyone involved in violence and vandalism.
Twenty-seven people have been arrested for their involvement in violence and lootings and 31 firearms have been found, it added.
Across various parts of the capital, military checkpoints have now been set up. On New Baneshwor street - the centre point of Tuesday's protests - officers are checking the IDs of any vehicles passing through.
One of the few sounds that can be heard is officers calling for people to stay at home.
"No unnecessary travel," their voices blare through a loudspeaker.
Still, some young people are out on the streets carrying bin liners and wearing masks, cleaning up the damage caused by the protests.
Among them is Ksang Lama, 14, who didn't attend the protests, but is hopeful it will lead to change in Nepal.
"This corruption thing has been in Nepal since a very, very long time, and I think it is high time that the nation needs to change," she said. "I really hope that it can bring something positive to our country."
Another supporter of change - 24-year-old Parash Pratap Hamal, who took part in Tuesday's demonstrations - says he is now cleaning up because they had caused "a lot of pollution".
He believes Nepal "needs independent political figures", he says - citing Kathmandu mayor Balendra Shah as someone who would make a good leader for the country.
The military is attempting to control a volatile situation, with Prime Minister KP Sharma Oli's resignation leaving a leadership vacuum.
His government's abortive attempt to ban social media triggered the demonstrations that saw 19 protesters killed in clashes with police on Monday.
Those deaths only fuelled the unrest on Tuesday, when three more deaths were reported. Two police personnel also lost their lives, the authorities say.
Scenes of violence and vandalism have come to illustrate the visceral intensity of the anti-government demonstrations.
Thousands of inmates have escaped from prisons around Kathmandu in the chaos, local officials told BBC Nepali.
Five young inmates were killed late on Tuesday when security forces opened fire at escapees from a juvenile correctional facility in Banke, in western Nepal. According to a director at the prison, they were all under the age of 18.
The military has invited the Gen Z protesters to engage in peace talks. Student leaders are consolidating a fresh list of demands, one of their representatives told the BBC.
But many protesters are worried that the movement has been co-opted by "infiltrators".
Tuesday's protest "organised by Nepal's Generation Z, was conducted with a clear vision: to demand accountability, transparency, and an end to corruption," read a statement issued by protesters.
"Our movement was and remains non-violent and rooted in the principles of peaceful civic engagement."
The authors of the statement said they were actively volunteering on the ground to "responsibly manage" the situation, safeguard citizens and protect public property.
They also said no further protests were scheduled from Wednesday onwards, and called on the military and police to implement curfews as necessary.
"Our intent has never been to disrupt daily life or to allow others to misuse our peaceful initiative," the statement said.
The army, too, has alleged that various "individuals and anarchist groups" had infiltrated the protests and were damaging private and public property.