The riot saw thousands of supporters of former president Jair Bolsonaro attack government buildings following his election loss last year.
The indictment says the individuals – who are not named – used violence and threats to try to abolish democracy.
Mr Bolsonaro has voiced “regret” for the unrest, but denies he caused it.
Perceived threats to democratic order are a sensitive subject in a country where military rule ended in 1985.
The far-right leader is currently in the United States, having left Brazil to avoid attending the inauguration of his successor – the veteran leftist politician Luiz Inacio Lula da Silva (widely known as Lula).
Lula’s election win in October outraged Bolsonaro supporters. Lula, a former president, was found guilty of corruption in 2017 and spent time in prison before his convictions were annulled.
Hundreds of arrests have been made following the 8 January violence – during which the presidential palace, Congress and Supreme Court were vandalised after rioters forced their way in.
Dozens of police officers were injured, and the scenes were condemned by President Lula and other world leaders.
Authorities in Brasília have pledged to more than double the security presence at locations that came under attack.
Monday’s indictment, presented to the Supreme Court, accused 39 people of offences including coup activities and damage to public property.
But the filing said it had not been possible to show the group had broken anti-terror laws – despite prior suggestions from the government that suspects could be charged on this basis.
The attorney general ordered a freeze on $7.7m of the group’s assets to cover repairs to damaged buildings.
During an address to a group of supporters in Florida, quoted by the Reuters news agency, Mr Bolsonaro called the recent scenes “unbelievable”.
In an apparent discussion of what happened, the former army captain said: “Unfortunately, people learned, understood what politics is, got to know the political powers, and started to value freedom”.
The Supreme Court has already said it will investigate whether the former president encouraged the violence – something he denies.
Mr Bolsonaro also faces separate probes over comments made while in office over alleged anti-democratic statements.
In his latest remarks, the ex-leader appeared to offer rare acknowledgement of errors during his presidency. He conceded: “There are some holes, of course, we make some slips at home.” bbc