There are concerns about the safety of schoolchildren who congregate in the area.
Drivers have also complained of congestion backing up to Vale Road and Pembury Road roundabouts.
Kent County Council [KCC] Highways has issued a warning about the conduct of pedestrians.
It said: “It is very clear that the majority of pedestrians heading towards the station are crossing Waterloo Road without taking due care for their safety.
“This is particularly true of the schoolchildren, who are crossing with little regard to the vehicles who now have right of way.
“Not only is safety an issue here but it prevents traffic from progressing even on a green light for them, leading to frustrated drivers and congestion on the system.”
The roadworks were completed last month. The state-of-the-art signals are designed to adjust their timings depending on the flow of both traffic and pedestrians.
But when the junction becomes blocked the signals reset back to their ‘worst case’ setting and stay on red longer than necessary.
To counteract this KCC will be installing yellow box markings in the junction to deter drivers from entering the junction without a clear exit, and will adjust some of the signal heads to help.
The pedestrian crossings will have additional displays higher up the poles and an extra push button on Waterloo Road.
A KCC Highways spokesperson explained: “As the lights use detection sensors, if people start crossing on a red man, the timer goes on longer and holds up the traffic.
“It is designed to do this for safety but it doesn’t help the whole system operate as efficiently as it can. When these changes have been implemented we can look again at the timings.”
The reconfigured road took six months to install as part of a £500,000 scheme that included wider pavements and narrower bus stops.
It is designed to help manage the flow of traffic, particularly at peak times when students are using the station and adjacent bus stops.
“We can now stop all traffic to allow the large groups of students to cross the roads in batches, which is a much safer way to manage the crossing than previously where students and vehicles would navigate around each other,” said KCC Highways.
“There are a number of tweaks we have recognised to the system that will improve its effectiveness which we plan to implement over the coming weeks.
“These include additional push button displays to really clearly show pedestrians when they should and should not be crossing the roads.”
