Crowds looted a warehouse believed to be storing food supplies for distribution during Covid lockdowns
Mohammed Adamu said criminals had hijacked anti-police brutality protests and taken over public spaces.
A new wave of looting was reported on Sunday, a day after Mr Adamu ordered police to end the "violence, killings, looting and destruction of property".
Protests calling for an end to police brutality began on 7 October.
The demonstrations, dominated by young people, started with calls for a police unit, the Special Anti-Robbery Squad (Sars), to be disbanded.
Comment: SARS. That's pretty ironic, given how The Covid plays into all this mass social unrest.
President Muhammadu Buhari dissolved the Sars unit - accused of harassment, extortion, torture and extrajudicial killings - days later, but the protests continued, demanding broader reforms in the way Nigeria is governed.
They escalated after unarmed protesters were shot in the nation's biggest city, Lagos, on Tuesday. Rights group Amnesty International said security forces killed at least 12 people. Nigeria's army has denied any involvement.
Lagos has in recent days seen widespread looting of shops, malls and warehouses, and property has been damaged, with the businesses of prominent politicians targeted. A number of buildings have been torched and prisons attacked.
On Sunday, there were reports of government warehouses being ransacked in the central city of Jos, as well as in Adamawa and Taraba states, with people taking away food and agricultural supplies.
There were similar reports of looting from warehouses in Bukuru city, near Jos, on Saturday.
The warehouses were said to have stored food supplies for distribution during lockdowns imposed to help control the spread of Covid-19.
President Buhari has said that at least 69 people have died in street violence since the protests across Nigeria began - mainly civilians but also police officers and soldiers.
On Saturday, the Nigerian police force tweeted that Mr Adamu, the inspector general of police, had told them "enough is enough" and ordered officers to "use all legitimate means to halt a further slide into lawlessness".
A group that has been key in organising the demonstrations in Lagos had on Friday urged people to stay at home.
The Feminist Coalition also advised people to follow any curfews in place in their states.
The group said it would no longer be taking donations for the #EndSARS protests.
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