Staff at Australia's domestic spy agency ASIO are expecting to move into their new $680 million headquarters more than a year and a half after it was officially opened.

Then prime minister Kevin Rudd opened the new building in Canberra last July, when it was not yet complete.

ASIO head David Irvine said the security and intelligence agency is in the hands of the building contractors.

"At the time the government made its decision [to open the building], I think it was July, the advice we had from the building contractors was it would be all ready for us to get the keys and start moving in ... doing our fit-out and everything else, at the end of August," he said.

"That is now ten months ago and you might detect a slight element of frustration in my saying that."

The five-storey building, named after former prime minister Ben Chifley, has been plagued by construction delays and its current cost is nine per cent above the original estimates.

The ABC's Four Corners program reported last year that the building's blueprints had been stolen in a cyber attack believed to have been mounted by hackers in China.

The enormous glass facade building on Canberra's Parkes Way remains empty and is surrounded by construction fencing.

Mr Irvine said the keys to the building will be handed over in mid-June for an ASIO specific fit-out, including particular wiring and security requirements.

"I am hoping that will not delay the ultimate entry into the building any further. The first cohorts should be going in towards the end of the year, early next year," he said.

Building size, cooling systems delayed handover

The nation's top spy says he has been presented with a range of reasons for the long delay.

Under questioning by Liberal Senator Zed Seselja in Senate Estimates, Mr Irvine said the automatic doors required a significant makeover and there had been problems with the chilling and cooling systems.

The ASIO director-general said the size and compartmented nature of the expensive new building had been a problem.

"That has then had an impact on the air conditioning and air pressure throughout the building, which in turn has an impact on fire, if there is a fire in the building.

"It has taken considerable time to work that out," he said.

"We are assured all [of] those matters will be addressed, or are being addressed, and we are proceeding now on the basis the end of next month will be for us the practical period where we can begin our work."

Remediation work on the building's air conditioning and fire control systems may still hold up the spy agency's plans.

Mr Irvine said ASIO has been given money for current rent and is not paying rent on the new building until it is occupied.

"In that sense the costs are neutral. Where the costs come is in the delay combining your staff into one building and all of the efficiencies that that provides," he said.

The ASIO building will eventually house the Australian Cyber Security Centre and will be dedicated to countering new threats.