Police arrested four people - three men and one woman - who hung banners from the roof of Parliament House that accused Australia of complicity in "war crimes" and "genocide".
Anthony Albanese slammed the actions of the protesters, saying their decision to breach parliamentary security "undermines our democracy".
"Those responsible should feel the full force of the law," the prime minister said.
"Peaceful protest has an important place in our society, but this was not a peaceful protest.
"People should be able to come and watch their parliament function in real-time but activities such as (the protest) undermines that."
House of Representatives Speaker Milton Dick said an investigation would examine how the protesters made it onto the roof.
"I've asked the commissioner for a wider review of security arrangements. I do not want a repeat of today's events," he said.
"We are deeply concerned about this morning's event."
Members of the public were barred from sitting in the House of Representatives during Question Time as a security measure following the protests.
Mr Albanese confirmed he had spoken with Australian Federal Police commissioner Reece Kershaw following the protests.
While the prime minister said he did not want unnecessary restrictions placed on access to Parliament House, the actions of the protesters had undermined their cause.
Opposition Leader Peter Dutton joined the condemnation of the protests.
"Serious questions need to be asked about how these people were permitted entry into the building," he said.
"We need to understand the gravity of the situation because these images will be beamed around the world."
Pro-Palestine protesters have been criticised for breaching security at Parliament House. (Lukas Coch/AAP PHOTOS)
Parliament House security was given a $126 million upgrade following a review in 2014, which resulted in a fence being built to stop public access to its roof without first going through security.
Senate president Sue Lines said matters of security at Parliament House needed to be taken seriously.
"There have been significant upgrades to security infrastructure and measures in the last parliament, and further upgrades are in progress," she said.
Australia's parliament was built into Capital Hill with a grassed roof, whose architect designed it to allow for people to symbolically walk above their elected representatives.
Foreign Minister Penny Wong said the protesters had "done nothing to advance the cause of peace".
The protesters who were arrested have been banned from Parliament House for two years.
They are expected to be charged with Commonwealth trespass offences.
