The ABC's Four Corners has reported cyber attacks netted documents that contained details of the massive new building's floor plan, communication cabling layouts, server locations, and security systems, potentially putting the entire organisation at risk.
The claims come amid deepening concern about widespread and aggressive state-sponsored hacking by China, with further allegations that its cyber spies have recently obtained sensitive Australian military secrets and foreign affairs documents.
Senator Bob Carr said that the government is "very alive" to cyber security threats, but refused to confirm the ABC's specific claims on Tuesday.
"I won't comment on whether the Chinese have done what is being alleged or not," he told Sky News.
"I won't comment on matters of intelligence and security for the obvious reason: We don't want to share with the world and potential aggressors what we know about what they might be doing, and how they might be doing it."
Senator Carr said that the claims did not jeopardise Australia's closer ties with the rising Asian power.
"It's got absolutely no implications for a strategic partnership," he said.
"We have enormous areas of cooperation with China."
Shadow Attorney-General George Brandis said that the government needs to properly resource all national security agencies to counter cyber attacks, amid new reports that recent public service efficiency measures have undermined their capabilities.
Senator Brandis said that Prime Minister Julia Gillard announced the formation of a new cybersecurity centre in January, but made no funding available to allow it to operate.
"I don't think, in view of the seriousness of the reports, a simple no comment is a sufficient response from the Attorney-General," Senator Brandis told ABC television.
"It's more than an operational matter because it goes to the integrity of the new ASIO headquarters."
The senator said he and his Liberal colleague Julie Bishop had sought an urgent briefing from ASIO head David Irvine for later on Tuesday.
Australian Greens leader Christine Milne said that there had been a security blunder of epic proportions and the government needed to explain itself.
"Everybody, of course, is aware in this century that cyber espionage is where it's at," she told reporters in Canberra.
"The government is now going to have to come out and explain to people how there won't be a long-term security impact, and what measures they are going to take to overcome whatever the damage is."
Independent Senator Nick Xenophon said that the government needed to be more open about what had happened.
"It seems now that the government is hiding behind the cloak of national security to cover up a very embarrassing situation," he told reporters.
"If it has been hacked by another country ... we need to know about that. Let's not be squeamish about this."