The organisation, which is trying to bring its radiation oncology waiting list back to normal levels after about 100 extra patients were added to it in April and May, saw patients within three months 73.9% of the time in the first quarter of the year, the ministry's figures showed.
Eleven DHBs reached or exceeded the 90% target they are meant to achieve, for an overall national rate of 90.4%.
South Canterbury (73.8%) and West Coast (72.2%) were the only DHBs to rank lower than Southern.
''The DHB has increased the amount of surgery undertaken over the last year, and has found it challenging to meet the targets,'' SDHB surgical services and radiology medical director Stephen Packer said.
Cancer Society Otago Southland division chief executive Rachael Hart said it was critical the SDHB improve its performance and achieve the cancer treatment target.
''Every day my team sees how important it is for patients to receive prompt attention in line with evidence-based guidelines,'' Ms Hart said.
''People in Otago and Southland should be able to expect treatment times that match the very best available in our country, and currently we're not achieving that.''
The faster cancer treatment target covers the time between referral and treatment for patients when there is a high suspicion of cancer, and the hospital doctor receiving the referral believes there is a need for an appointment within two weeks.
Dr Packer said about 70% of people were treated by surgery, and the SDHB was sending some patients to private hospitals to try to improve its performance.
''We continue to work on strategies to ensure we see and treat our patients within the Ministry of Health recommended timescale.
''These include nurse-led clinics, travelling clinics, electronic referrals and triaging, additional theatre sessions and combined clinics for out-of-town patients.
''We are aware we have a large challenge to develop these strategies to serve us into the future with the continuing increase in demand.''
The most recent health target data was posted on Parliament's website recently, in response to written questions by National health spokesman Michael Woodhouse, who also asked Health Minister David Clark when he expected new health targets would be in place.
''It is my aim to have a robust set of measures in place as soon as practicable,'' Dr Clark said.
''It is important that these new measures are robust and fit for purpose, and that they align with government priorities.
''While they remain under active development, health target measures continue to be collected and reported on.''
