The board said the women's care was unaffected, because reports written from the mammograms were intact.
The 3850 women were advised by courier letters on Tuesday and yesterday, and the board has set up an 0800 number.
The mammograms were taken between February 1, 2012, and October 31, 2012.
Chief executive Carole Heatly said the failure was an IT server issue, unrelated to the department's longstanding problems caused by lack of radiologists.
The board became aware of the botch-up in June last year, but said nothing because it had to go through every patient's file to try to retrieve data. Some images were retrieved in that process.
Counties Manukau District Health Board, which has been supporting the unit, was contacted to determine what images it had saved.
The incident was being treated as a learning experience, and no disciplinary action would be taken.
''This is about us being open and transparent. We lost some information details pertaining to patients, and we feel we have a responsibility to let the patients know that that happened.''
University of Otago screening authority Associate Prof Brian Cox, when contacted, said he believed there would be a small increase in the number of biopsies performed, notwithstanding the fact clinical reports had been taken.
This was because initial screens were sometimes referred to, rather than clinical notes.
However, clinical outcomes would not be affected and biopsy was a low-level procedure, he said.
Prof Cox said screening programmes handled huge amounts of data.
The lost mammograms could affect the programme's ability to audit the service for quality control.
Asked to respond, Ms Heatly said her advice from clinicians was there would be no change to the women's care.
''I would like to apologise to the 3850 people who received a mammogram in Southland during this time and whose images have been lost.
''The images were lost due to an incorrectly configured server which failed to back up the copies of the images, thereby losing them.
''We want to reassure all patients that there is no change in the outcome from those mammography images. All lost images had been read by doctors and their reports remain in each person's clinical file,'' Ms Heatly said.
The board's contract for the national breast-screening programme is being outsourced, because it is not considered sustainable, while the diagnostic breast-care service will stay in-house.
The IT loss affected both diagnostic and breast-screen programme mammograms.
A National Health Board spokesman said yesterday the BreastScreen Aotearoa contract was still under negotiation.
