A 20-year-old man has been arrested and charged after Brisbane's City Hall was vandalised with large letters in white paint spelling "SOVEREIGNTY" and an Indigenous flag logo overnight.

The letters were painted between the doors of the heritage-listed City Hall overlooking King George Square overnight on Monday.

The hours-long removal of the white paint from the front of Brisbane City Hall starts. Credit:Lucy Stone/Fairfax Media

Council workers began scrubbing the graffiti off the sandstone in the morning, with the flag logo removed by 11am.

Workers later covered the remaining letters with white board as the clean-up continued.