Canberra Metro has moved its operational commencement date from December 21 this year to January 2019, although both the consortium and Transport Canberra warned it could change.

The delay was made public after Transport Canberra's latest annual report showed the project missed nearly all of its milestones by several months.

Transport Minister Meegan Fitzharris said on Monday the government was not in a position to confirm the official start date as her directorate was still waiting on information from Canberra Metro.

But Under-Treasurer David Nicol told annual reports hearings on Monday the government had also been unaware of the delay in the program until recently.

“I have to take on notice the exact timing of the sequence of events. It’s only been very recently that the contractor has informed us that the project would now likely start in the new year rather than this year but I can take on notice the exact date that information was communicated to us," Mr Nicol said.

“How is it that you knew only relatively recently the project was running late? Didn’t the milestones weren’t being met give you a pretty good indication the project was running late?" ACT Opposition leader Alistair Coe asked.

"The contractor maintained a 21 December commencement operations start date, we had been asking questions for some time of the contractor to make sure that was achievable and it’s only recently that the contractor has revised that date," Mr Nicol said.

A spokeswoman for Ms Fitzharris said the government was told about the delay at the end of October, but did not provide a date.

Mr Coe then asked whether there were any unresolved contract variations that threatened to have an impact on the cost of the project.

"That will depend on how they’re resolved but there could be sums of money involved, yes," Mr Nicol said.

According to the contract with Capital Metro, a territory-retained risk contingency of $117 million is built into the $707 million set aside for the design and construction of light rail.

A government spokeswoman last month told The Canberra Times the territory was yet to pay any contingency amounts to Canberra Metro.

"To date there have been some relatively minor agreed modifications with Canberra Metro that have effectively cancelled each other out," she said.

Mr Nicol said a number of changes to the project scope had already been approved, such as changes to the design of the stops.

"Not a significant number but a number," Mr Nicol said.

Ms Fitzharris' spokeswoman said compared to similar projects in other jurisdictions, the ACT government had been "especially disciplined" in minimising the number of project minimisations along the way.

"As expected though, there have been some modifications over the past two years. There have been 45 modifications agreed to date, though 28 of them do not have any cost impact. Of the remainder, they’ve had both positive and negative values," she said.

"For example, the ACT government issued a modification to include additional smoke detection systems in the light rail vehicles and another to enhance street lighting on Hibberson Street. They are well within the forecast $707m project cost."

The spokeswoman confirmed other variations were still being negotiated, although weren't expected to blow out the budget.

"This is entirely expected given the nature and complexity of the project. These relate to a variety of topics, including Northbourne Plaza and contract interpretation questions. We expect these to be resolved in due course," she said.

"The ACT government and Canberra Metro maintain a very constructive working relationship and our current discussions are neither unusual nor unexpected. We expect discussions to be finalised in due course, noting that we do not anticipate those discussions will be prolonged."