"We think this is a sensible sequencing of enabling works which will minimise disruption of critical intersections in the CBD and enable compliance with the planning conditions that only one intersection can be out of action at any one time," it has told Mr Bridges.
"A more compact construction schedule at a later time would prove too disruptive."
The agency also discusses a possibility of the major construction phase, of bored tunnels to Mt Eden and the construction of two underground stations, starting as early as 2018 - and being completed by 2022 for around $2 billion.
Despite Prime Minister John Key's signal last year that the Government would consider supporting a pre-2020 construction start only if ambitious patronage and employment creation targets are met, the agency has indicated concern about missing out on an earlier start.
"The risk of not being involved in these early stages is that the key elements of the project get determined in the meantime," it says.
"If the Crown is to be a future funding partner, it needs a mechanism to identify options and risks around planning, design, procurement and financing."
The agency has suggested to Mr Bridges a possible role for itself as a technical partner with Auckland Transport in development the project, to help to "manage Crown risk."
"This would be consistent with the one transport system arrangements that have been forged with Auckland Transport and Auckland Council over the last 3-4 years."
It has also highlighted to the incoming minister its own experience in complex infrastructure undertakings of the scale of the rail project.