It would be trialled until the end of the year then reassessed.
The service comes at the cost of Sunday and public holiday services between Raglan and Hamilton, and higher fares.
"The $18,000 was the difference required to meet the change and that's coming out of existing budgets which are now being squeezed further, obviously, because we had no more money ourselves."
The last Sunday and public holiday services on the route to Raglan operated over Queen's Birthday weekend.
Mr Smith said that although everyone's needs could not be met, he believed the trial was the best outcome.
"We recognise that not everybody is happy, but the communities in Raglan and Whatawhata asked us to come up with something. This is the best where the majority of the needs are met.
"It's the best outcome for the short to medium term and it gives us six months to work on the longer term options because we know that more people in Raglan are choosing to send their children to school in Hamilton and that's the underlying issue that we as a council can't change."
He said the next aim was to get the two buses leaving the transport centre at the same time "so people going to Whatawhata don't get on the Raglan bus and take up seats".
The Raglan bus now left at 3.40pm, and the Whatawhata bus departed 20 minutes later at 4pm.
"If you have a 20 minute delay people will naturally say 'oh to hell with it, I'm getting on that bus because I can get home 20 minutes earlier'."
The Waikato Regional Council had been asked to align the services as soon as possible, Mr Smith said.
But for now on school days, a 20-seater bus will depart Glentui Lane at Whatawhata at 7.15am, arriving at the Hamilton Transport Centre about 7.50am.
It will return from the transport centre at 4pm, arriving at Glentui Lane about 4.40pm.
ON THE BUSES
* $18,000 from Waikato District Council
* $33,000 from Waikato Regional Council
* Trial to run until the end of 2012
* Aimed at easing overcrowding on Hamilton to Raglan bus for school students.