Mass arrest in Brazil as Lula condemns 'terrorist' riots
The rioting came a week after President Luiz Inácio Lula da Silva was sworn in.
He condemned the "terrorist acts" and vowed to punish the perpetrators.
Mr Bolsonaro has not admitted defeat and flew to the US before the handover ceremony. Unconfirmed reports say he is in a hospital in Florida.
The new president - widely known as Lula - and the heads of Congress and the Supreme Court "reject the terrorist acts and criminal, coup-mongering vandalism that occurred" during the riots.
The dramatic scenes saw thousands of protesters clad in yellow Brazil football shirts, and flags overrun police and ransack the heart of the Brazilian state.
Lula was forced to declare emergency powers.
On Monday morning, heavily armed officers started dismantling a camp of Mr Bolsonaro's supporters in Brasilia - one of a number that has been set up outside army barracks around the country since October's election.
Brasília's Civil Police said an additional 300 people were detained on Sunday.
Justice Minister Flavio Dino said some 40 buses which had been used to transport protesters to the capital had been seized.
Mr Bolsonaro condemned the attack and denied responsibility for encouraging the rioters in a post on Twitter some six hours after violence broke out.
Meanwhile, Brasília governor, Ibaneis Rocha, has been removed from his post for 90 days by the Supreme Court.
Justice Alexandre de Moraes accused him of failing to prevent the riot and of being "painfully silent" in the face of the attack. Mr Rocha has apologised for Sunday's events.
A video shared by the Brazilian outlet O Globo showed some officers laughing and taking photos together as demonstrators occupied the congressional campus in the background.
Some protesters smashed windows, while others reached the Senate chamber, where they jumped onto seats and used benches as slides.
Protesters had been gathering since the morning on the lawns in front of the parliament and up and down the kilometre of the Esplanada avenue, which is lined with government ministries and national monuments.
Despite, in the hours before the chaos, security had appeared tight, with the roads closed for about a block around the parliament area and armed police pairs guarding every entrance into the area.
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