"I have yet to see any expert opinion or analysis to date which indicates that the burqa or the niqab represents an additional or special security threat."
Read more: Abbott backtracks on 'confronting' burqa comments
Labor opposition frontbencher Tony Burke welcomed the backdown but said the initial decision should never have been made.
"What possessed them to think that segregation was a good idea?" he said.
"Segregation was previously introduced, apparently, with no security advice attached to it and no security reason attached to it."
The Department of Parliamentary Services said in a statement that the rules had been changed and all visitors must now "temporarily remove any coverings" that prevent the recognition of facial features.
"This will enable security staff to identify anyone who may have been banned from entering the building or who may be known to be a security risk," it said.
"Once this process has taken place visitors are free to move about the public spaces of the building, including all chamber galleries, with facial coverings in place."
Australia has been on edge since the rise of Isis (Islamic State) with the government tightening counter-terrorism laws and police in recent weeks conducting major terror raids amid fears of an attack on home soil by radicalised Australians.
The country was one of the first nations to join the United States' aerial campaign against the militant group, which controls large parts of Iraq and Syria and is increasingly seen as a global threat.
On Sunday, Canberra said it had reached a deal with Baghdad for the deployment of about 200 special forces to assist Iraqi troops in their fight against jihadists.
- AAP