He has been appointed a Distinguished Companion of the New Zealand Order of Merit, an honour shared with three others: Wellington historian Dr Claudia Orange, Auckland businessman John Wells, who chairs Sport and Recreation New Zealand, and former Speaker of the House Margaret Wilson.
The highest honour went to Prof Ngatata Love, of Porirua; appointed a Principal Companion of the New Zealand Order of Merit for services to Maori.
Prof Skegg, who has led the University of Otago for four years, is among 19 southern people honoured.
They include broadcaster and Dunedin city councillor Neil Collins, who was made an officer of the New Zealand Order of Merit; Invercargill artist John Peninsula (Member of the New Zealand Order of Merit) and former Police Southern Area commander Deputy Superintendent Nick Perry (Member of the New Zealand Order of Merit), who is now working at the New Zealand High Commission in London.
Among southerners to be awarded Queen's Service Medals were Monica Burns, of Invercargill, Dr Mike Floate, of Cromwell, and Lindsay Malcolm, of Oamaru.
University of Otago staff members featured prominently in the southern list, among them Emeritus Prof Jocelyn Harris (Companion of the New Zealand Order of Merit), and senior staff members Prof Harlene Hayne and Prof Geoff White (Members of the New Zealand Order of Merit).
Prof Skegg's New Year honour has been awarded for services to medicine, principally his many years of research into breast and cervical cancers and his interest in improving the safety of medicines.
Although leading an organisation as large as the University of Otago was a "seven-day-a-week job" - there are four campuses, about 20,000 students and more than 3000 staff - Prof Skegg said he had made time to continue his research.
"At the start I tried to set aside Friday afternoons, but that didn't really work . . .
"But I am still working on some collaborative projects with colleagues from the medical school in Dunedin and with colleagues internationally, and still manage to publish a few papers each year.
"I was determined to make time for it, really."
Asked how he felt about his latest distinction, Prof Skegg was modest.
"I feel very honoured, but I can't help feeling there are many other people who deserve it more than I do."
While he said he was "thrilled at the way the university was going", he did not see his New Year's honour as being connected with his university leadership: "It has been awarded for services to medicine, not for services to the university."
He said his research achievements and the university's success were the work of many people, not just himself.
His current projects continued his long interest in cancers and the safety of medicines, he said.
He has also just been appointed to a World Health Organisation advisory committee on reproductive health in developing countries.
Born in Auckland, Prof Skegg graduated from Otago with a BMedSc, MB, and ChB with distinction, and was awarded a Travelling Scholarship in Medicine and a Rhodes Scholarship to Balliol College, Oxford.
After graduating with a DPhil, he remained at Oxford as a lecturer in epidemiology from 1976-79, returning to Otago in 1980 to take up the chair of preventive and social medicine.
Prof Skegg has been involved with several international committees including chairing a breast cancer research group centred at Oxford, and adviser to the World Health Organisation's human reproduction research and development programme for more than 15 years.
In 2002 he gained world-wide attention as co-investigator in a major study which debunked claims that vasectomy is linked to prostate cancer.
He was awarded an OBE in 1991 and made a Fellow of the Royal Society of New Zealand the following year.
