Acting Chief Executive Eric Chan said police have been asked to investigate an incident at the Western Harbour Crossing on Monday that led to thousands of drivers being overcharged.

Speaking to reporters ahead of the Executive Council meeting on Tuesday, Chan said according to an initial probe by the Department of Transport, human error was to blame for the problem, which lasted for around an hour and affected about 4,700 vehicles.

He said the government is highly concerned about the case and that police will investigate.

"We suspect that there is undue interference by somebody... So, we are leaving the matter to the police," Chan said.

"If this is a deliberate attempt to interfere with the system, then it is definitely a criminal act and the relevant individual will of course be brought to justice and feel the full force of the law."

He added that some 3,400 drivers have been issued refunds after they were charged the wrong toll.

The incident came a day after the introduction of new dynamic pricing at the three harbour tunnels, with varying fees for private cars and motorcycles depending on what time of day they travel.