The rise came in the wee hours between midnight and 6 am on Monday after the government took over the tunnel on Saturday, when a new time-varying toll and a switchover to HKeToll were also implemented.
Charges for all vehicle types were reduced by 22 to 80 percent under the new regime.
Private cars are charged HK$45 during peak hours, HK$30 during regular periods and HK$18 during off-peak periods from Monday to Saturday.
A flat rate of HK$18 is implemented throughout Sundays and public holidays.
Speaking after a tunnel inspection, Mable Chan said she hopes the new arrangement can alleviate congestion on Tuen Mun Road by 5 percent.
“Traffic was up by about 40 percent when compared to the average flow on Sundays,” she said.
“This was within our expectations because private cars are now charged HK$18, a significant drop on the previous HK$58 charge.
“So far the traffic situation is within our expectations and under control.
“We hope that cars will opt for Tai Lam Tunnel as this will help alleviate peak-hour congestion on Tuen Mun Road.
“We hope traffic on Tuen Mun Road can be cut by 5 percent during peak hours.”
The Transport and Logistics Bureau will closely monitor the traffic situation, Chan said.
The government, she added, will review charges for its tunnels and consider looking into those for Aberdeen and Shing Mun tunnels first as they have remained unchanged for years.
It will also look into imposing a charge for the Central Kowloon Route that is set to be completed by the end of the year to recover costs, she said.
She added that her bureau will brief lawmakers on the review on tunnel tolls this month.