Contractors and their workers were subject to ASIO security screening and signed declarations acknowledging they faced years in jail or six-figure fines if they talked publicly about the $631 million job.

A ''building project team'' of ASIO operatives kept an eye the workforce throughout the construction period and several workers were frogmarched off the lakeside site and told not to come back after they inadvertently broke the rule requiring mobile phones to be checked at the gate.

But ASIO has denied the persistent talk in the industry that intelligence officers disguised as labourers roamed the site throughout the long construction period.

The Gillard government faced a political storm on Tuesday after ABC's Four Corners program broadcast an unsourced claim that detailed blueprints and security plans for the lakeside site had been stolen from a contractor's computer with the security breach traced to China.

Local construction sources have told Fairfax Media that "sanitised" onsite computers were provided for contractors, that all plans and blueprints they used were hard copies and were not allowed to leave the site.

The TV program claimed the hacking was one of the reasons for the delay to the $633 million building, which has also been dogged by insolvencies among contractors that have descended into bitter disputes with project builder Lend Lease.

Both ASIO and Attorney-General Mark Dreyfus declined to comment on Tuesday but Prime Minister Julia Gillard told Parliament the ABC report was ''inaccurate'' and contained ''unsubstantiated allegations''.

''As the Attorney-General has stated, neither he nor the director-general of ASIO intends to comment further on these inaccurate reports in accordance with the longstanding practice of both sides of politics not to comment on very specific intelligence matters,'' she said.

Greens leader Christine Milne called for an independent inquiry into the project, which is now nearly a year late and $171 million over budget, calling it a "sorry saga".

"It is a legacy of the Howard government and has been carried on by the Gillard government," Senator Milne said.

"It's time we had an independent inquiry into the history of the ASIO building and the extent to which the current hacking has compromised its capacity to ever be the building and serve the purpose for which it was intended - home of the Australian Security and Intelligence Organisation.''

Independent senator Nick Xenophon said: ''It seems now that the government is hiding behind the cloak of national security to cover up what seems to be a very embarrassing situation.''