Money raised from increases to fuel taxes is expected to generate close to $100 million this financial year.
Road user charges for diesel vehicles went up on Thursday by varying amounts based on vehicle weight.
The excise duty on petrol also rose three cents a litre to 45.5 cents a litre.
Transport Minister Steven Joyce says revenue from the increases will go into the National Land Transport Fund, to pay for new roading projects, maintenance, policing of the roads, and some public transport subsidies.
Several oil companies say they will wait as long as possible before passing on the three cent petrol excise increase to their customers.