The result was called "disturbing" by Southern DHB member Richard Thomson, at the hospital advisory committee meeting last week.
And he found it "really grot" the compliance target was 70%, which sent the wrong message.
Hand hygiene means either traditional hand-washing or applying an anti-microbial agent without water.
Figures provided to the Otago Daily Times show doctors' compliance was about 40%.
They only outranked cleaners, orderlies, tradesmen and other miscellaneous staff, of whom 30% cleaned their hands.
Hand-washing was likely to be introduced as an official national health target, increasing its prominence and public awareness, chief medical officer David Tulloch told the meeting.
Chief executive Carole Heatly said patient pressure was brought to bear on clinicians in the United Kingdom, where she worked until last year - patients asked the doctors "have you washed your hands?"
The "huge issue" of hospital-acquired infections in the National Health Service prompted the campaign.
A culture change saw clinicians either roll up their sleeves or wear short-sleeve shirts so they had clean and bare lower arms.
It was not just about meeting health targets but a "promise to the people 'we will wash our hands'," Ms Heatly said.
Contacted after the meeting, Mr Tulloch said through a spokeswoman the national average for hand hygiene compliance was 63%, which included DHBs "working on this issue for longer".
A breakdown of other staff in the Dunedin Hospital audit showed health-care assistants were most likely to clean their hands (nearly 80%); allied health staff (nearly 70%); nurses (nearly 60%); phlebotomists and students (about 45%).
"Dunedin Hospital was part of the second phase of the Hand Hygiene New Zealand roll-out, so culture change around all aspects of hand hygiene best practice is still developing," Mr Tulloch said.
Hand hygiene was still a "relatively new initiative" in New Zealand. The DHB was reviewing where hand-cleaning products were placed to ensure easy access.
The audit result was received by the Southern DHB about a fortnight ago, a spokeswoman said.
The five "moments" for hand hygiene
• Before touching a patient
• Before a procedure
• After a procedure or body fluid exposure
• After touching a patient
• After touching a patient's surroundings
Source: www.handhygiene.org.nz
