The head of the new agency Major Projects Canberra estimated it would need an additional $5 million funding a year to run the office, suggesting it take unspent funds from Canberra Hospital's SPIRE project or light rail stage two to meet its corporate costs.

Major Projects Canberra was launched on July 1 last year, charged with overseeing the territory's major infrastructure projects. Chief Minister Andrew Barr said at the time the agency would be entirely funded through the existing budget for the territory's public service.

But even after the agency was live, how it was to be funded and how it was to remain "budget neutral" was yet to be determined, internal emails released under freedom of information reveal.

On July 3 last year, interim head of the agency Duncan Edghill said in an email to senior treasury staff that the "unresolved funding" could be more than $5 million a year.

He suggested a way to solve the problem was to take unspent funds from Canberra Hospital's expansion project SPIRE or light rail stage 2 to pay for the running of the office.

"As you'd be aware, Major Projects Canberra will need to incur costs associated with its corporate functions such as accommodation, audit, systems, governance staff and so forth (including my salary) - noting we've been established as a stand-alone agency," he said.

"The funding source has not yet been finalised for Major Projects Canberra in respect of these costs."

Mr Edgill noted that taking money from light rail or SPIRE would only address the funding matter for 12 months.

"The advantage of it is that would enable the new organisation to settle and gain a firmer handle on its actual corporate costs ahead of 2021-21," he said.

He said other solutions could be getting a mid-year funding boost, or contributions from other relevant directorates. Treasury staff balked at the $5 million figure put forward by Mr Edghill.