Bikes will be separated from traffic by 40cm wide concrete kerbs, similar to those already used on the cycleway.
The application for resource consent has been publicly notified, and people are able to submit on the application. Submissions close on June 23.
Auckland Transport cycling, walking and safety manager Kathryn King said the cycleway extension will make the waterfront safer for cyclists heading into the city from East Auckland.
According to Auckland Transport, the cycle route into the city via Tamaki Drive and Quay Street has more trips per day than the pink Lightpath and the Northwestern cycleway.
Auckland Transport estimates the earthworks will cover about 450sq m, up to a depth of about 0.5m to build the extension to the cycleway.
In addition to moving the trees, a bus stop will be relocated, a ramp will be installed and the median island in the middle of Quay St will be narrowed.
About 18 car parks will be removed from the northern side of Quay St, opposite the shopping area.
The Quay St cycleway was opened in July last year, and according to Auckland Transport has had more than 50,000 cycle trips since then.
It is a mix of on and off-road two-way cycle lanes, and is about 3m wide.
Auckland Transport, Auckland Council and the Government are all contributing to a $200 million programme of cycle improvements in Auckland from 2015 to 2018.