The hospital has about 700 paintings, sculptures and installations in its collection, ranging from its prized Robin White Seven Hills mural to bargains unearthed in second-hand shops.
Some art works had been lost from the "highly valuable" collection, chief operating officer Vivian Blake told the Otago District Health Board last week.
An electronic database of the collection is being created, which has photographs of the art works, the name of the artist, the location and value of the works.
Art cataloguer Kristin Collins told the board some art works had been "lost in an office for 22 years" or moved around and "no-one is sure where they went".
However once the catalogue was completed, up-to-date records could be kept of art works' locations and no more works should be lost.
Controversy has surrounded some sculptures in the past, one of which involved a John Middleditch copper fountain sculpture being stripped back and polished.
Middleditch was a Dunedin sculptor who deliberately gave his copper works an aged appearance.
About 70 of the most valuable works in the collection are owned by the HealthCare Otago Charitable Trust and the rest are owned by the board.
Board member and arts advisory committee chairwoman Judith Medlicott told the Otago Daily Times many of the art works had been donated to the hospital.
She would not disclose the value of the collection, but it has many works by respected contemporary New Zealand and Dunedin artists.
It was first started in the 1970s when the late Prof Alan Clarke returned from overseas where he had noticed the value of art works in hospitals for patients.
Mrs Medlicott said patients often commented on how art works provided a welcome distraction and people often donated art after a stay in the hospital.
Committee member Gordon Sanderson said some paintings had been damaged in the past - Robin White's mural was protected with perspex and and a guard rail after somebody punched a hole through it - but it was important to have them on display.
"People have got to have access to them or there is no point in having them."
Walking around the hospital could be a real delight as significant works were tucked away in funny places.
Just taking people on a tour of works on the ground floor took more than one hour, he said.
