In the statement, the Agency said ramp signals were just one tool to manage traffic.
Quoting Highway Manager Brett Gliddon, the statement said the traffic lights could end up being used infrequently.
They didn't expect significant queues, and he said claims of gridlock were "misleading".
The traffic lights will also be used to prevent traffic entering the tunnel if there is an accident.
"Best practice across the world for managing tunnels is to have the ability to limit the amount of time traffic spends queuing inside tunnels," Brett Gliddon said.
"The ramp signals are not operated in isolation, and are designed to be controlled by operators who are managing the entire road network."
The Agency said travel information and social media would also be important to spread travel times, and information about alternative routes.