Tolls for the Aberdeen and Shing Mun runnels rise from HK$5 to HK$8 from Sunday.
In a statement, the Transport Department said the new tolls are to help tunnel operations to "largely attain break-even".
The department also reminded the public that charges for metered parking spaces will be up from HK$2 to HK$4 per 15 minutes starting next Sunday.
It added fees for metered parking spaces for goods vehicles, buses and coaches would remain unchanged.