The St Clare's College website was hacked to display white Arabic text on a black background with "scary" music playing in an apparent reference to Islamic State over the weekend.
The school is reviewing its security to avoid a repeat of the incident, but principal Paul Carroll said all student information and college data was kept secure despite the website's "face" being compromised for about one hour on Saturday.
A former student's father, who declined to be named, said he contacted the National Security Hotline after his daughter showed him the website.
"The background was all black and there was scary music with an IS [Islamic State] flag at the top," he said.
"It was this dark, frightening, Islamic thing with something about threats to non-Muslims."
Mr Carroll said the school's IT staff restored the website as soon as they were alerted to the attack and the National Security Hotline was informed, but there were no threats to students or staff.
"There was no personal message to me or anyone here … because of the [Arabic] language on the front it suggests it was a crusade to attack people from all over the place," he said.
"There was some English that said: 'you've been attacked', 'you've been hacked' and it also had it in Arabic."
The girl's father said it was sad to see the school harassed in such a "violent way" especially with its 50th birthday celebrations approaching.
"What has that school ever done that was anti-Muslim?" he said.
"For sleepy little Canberra it's a bit of a shock to see that on the website of a quiet girls' school in Griffith."
Mr Carroll said the combination of Arabic and English text used on the website suggested the hacking originated from the Middle East or Pakistan area, but he did not see the messages before they were removed.
He said the website appeared to be have been attacked at random and he did not believe it was because of the school's Catholic denomination.
"It's not unusual for these things to happen," he said.
"They'll be doing it to other websites across the world. It's just a nuisance."
"We didn't read anything into it individually."
Mr Carroll said the school always reviewed its security, but a commercial IT team had been hired to investigate current security arrangements to avoid a recurrence.
"This is going to be part and parcel of technology," he said.
"There are always people spending their lives being a nuisance if they have the time and resources."
He wrote to parents on Monday explaining what happened and saying there was "no cause for alarm".
An ACT Policing spokesman said the incident was not reported, but anyone who suspected a private website had been hacked should contact the Australian Cybercrime Online Reporting Network.
The Hobart International Airport website was hacked with a statement supporting Islamic State last month.
At the time Tasmania Police said thousands of identical messages had been posted on websites worldwide since late 2014.
Last week, a Canberra woman claimed her teenager's Facebook account had been hacked by a member of Islamic State, but the incident was found to be a false alarm.