The Otago Regional Council attributed the cancellations to "driver illness" although its operators are still 10 drivers short.
Compared with last winter, the situation had improved, the council said.
Interim transport manager Doug Rodgers said 6.5% of trips were cancelled as of 3pm yesterday, compared to a pre-reduced timetable cancellation rate of over 10%.
"Teething issues were expected in catering to public demand for a return to full timetable services," he said.
"Our operators are 10 [drivers] short of an optimum number to service the network fully."
Last August, the council said 38 drivers were still needed.
The council wanted to provide certainty for those using public transport amid the ongoing flurry of cancellations.
Operational changes minimised the impact of the driver shortage, Mr Rodgers said.
Four more drivers were due to start work mid-February.
"Teething issues with the new timetable are expected to continue in the interim until new drivers are on board."
People were advised to check cancellations on the council web page before travelling.
The arrival of two cruise ships in Port Chalmers yesterday also put more demand on bus services, and the council put up signs advising cruise ship passengers to give priority to elderly, children and school students.
"Five buses were on the route today compared to single buses in a normal day.
Interim chief executive Pim Borren said staff and bus operators had put in a phenomenal effort to be back on a full timetable by February 1, ahead of all other urban centres in the country.
Dunedin Tramways Union secretary Philip Mathews said yesterday was a busy day, as expected.
"On the whole it went well— yes, there were delays, but a lot were due to roadworks," he said.
Despite the disruptions, bus users who spoke to the Otago Daily Times yesterday were pleased the full service had been reinstated.
Nele Tili said her bus, the number 38 to Concord, was running 15 minutes late and she did not know when it would come.
The hospital worker was "waiting, waiting, waiting" at the central city bus hub, but said the council was correct to bring back the full timetable.