Published tomorrow, the NAO report is expected to be highly critical of the London building's £1 billion refurbishment, which was launched seven years ago by former BBC director general Greg Dyke.
According to figures seen by The Guardian, the BBC West One project is now £59m over its original budget of £990m set in 2003.
The redevelopment, which aims to create a new base for all BBC News, World Service and radio operations, saw its budget revised to £1.04bn in July 2007.
Buildings around the back of Broadcasting House have already been demolished to create space for a huge newsroom facility, while five studios will host programmes such as Newsnight.
Licence fee payers will be able to watch BBC journalists at work from the main foyer, but the corporation has been forced to balance the desire for transparency with security concerns.
Chris Kane, head of BBC Workplace, told the newspaper that fast-paced change in digital and broadcasting technology has also created headaches for the development.
"It's the first time we've put all our news services together," he said.
"The concept is to create a space where all of the creative elements of journalism sit together to collaborate. It's the building that never sleeps."
Around 4,500 employees will be working at the new BBC Broadcasting House by spring 2011, with teams moving from Television Centre and Bush House.