Eyewitness video showed black smoke billowing from the entrance of the building.
The fire engulfed the front doors before it was put out. No one was injured during the process, local media reported.
Australian Capital Territory (ACT) police had agreed to what was supposed to have been a "small smoking ceremony" by protesters, but according to ACT police commander Linda Champion, it had gotten "a little bit out of hand," local media reported.
Indigenous rights campaigners had been protesting outside the building for weeks in the build-up to the 50th anniversary of a permanent protest occupation site for Aboriginal rights, which is located on the lawn opposite the Old Parliament House.
Government lawmakers and Prime Minister Scott Morrison condemned the protesters' actions.