Vogel St in Dunedin is preferred as the route for cyclists riding into the city from the south once the one-way cycleway system is complete.
However, the NZ Transport Agency says its cycleway on Crawford St will remain in place.
Cyclists coming from the south will need to cross from either street to a two-way section of cycleway across the road from the Toitu Otago Settlers Museum before connecting to the cycleway that will run north on the right-hand side of Cumberland St.
NZTA projects team manager Simon Underwood said the work being done at the Queen's Gardens area was complex, as part of it was bi-directional, taking cyclists in both north and south directions.
When the cycleway was complete, the NZTA wanted cyclists coming from the southern suburbs to use Vogel St so they could easily connect, though the cycleway on Crawford St would still be available.
Mr Underwood said that would be done using a ''hook treatment' as was already in place at Stuart St, allowing cyclists to cross the highway at traffic lights.
At the intersection of Stuart St and Castle St, cyclists have an area to pull off the road to press a button and wait for a special cycle light that tells them when they can cross from the left to the right-hand side of the road.
The cycle lane there is on the left of the road, but will change to the right once the cycleway work is completed.
The Dunedin City Council completed work on Vogel St in 2015 to improve it for cycle and pedestrian use.