The facilty at the Royal Infirmary of Edinburgh – where surgical instruments are cleaned and prepared in an ultra-clean environment – serves the whole of NHS Lothian.
The closure forced the postponement of planned and non-emergency surgery on Friday and across the weekend and will mean no routine elective procedures can go ahead.
Procedures in NHS Lothian will now be disrupted for a minimum of two to four weeks.
The health board said more urgent surgery would be considered daily on a case-by-case basis to prioritise the most clinically urgent.
HSDU is the facility where surgical instruments are cleaned and prepared for surgery. An ultra-clean environment is essential.
Tracey Gillies, NHS Lothian medical director, said: “We are sincerely sorry to all patients who have been or who will be affected by this problem.
“The decision to postpone any operation is never easy as we know how disappointing and stressful that can be. Unfortunately, it is essential in order to ensure sufficient clean surgical supplies are available for emergency operations.
“Patients will be contacted by their clinical teams if their procedure is to be postponed and they will be notified as soon as possible of rescheduled dates for their surgery.”
Support has been offered by several other health boards such as NHS Lanarkshire and their HSDU operator, Steris, which are providing replacement supplies of the surgical instrument trays used in operating theatres.
NHS Greater Glasgow and Clyde has also offered the use of its HSDU facility to carry out sterilisation and decontamination of NHS Lothian’s instruments.
NHS Lothian chief executive Calum Campbell said: “We are very grateful to NHS Greater Glasgow and Clyde (NHSGGC), NHS Lanarkshire and the other boards who have all offered support.
“My thanks also go to our HSDU staff who are travelling back and forth to Glasgow to work at NHSGGC’s HSDU to help maintain our supply of clean surgical trays.
“These measures mean we will remain equipped for emergencies and can continue to carry out some planned surgery.
“However, although we are continuing to explore additional contingencies, regrettably, even with this help, there is likely to be significant disruption to our surgical lists while we work to rectify the damage and reopen our HSDU.”
The water leak, which came from a drainage pipe, resulted in small puddles of water forming on the floor and damp areas where the walls meet the floor.
A full assessment is still underway. However it is thought work to fix the leak source, rectify the damage, test and re-open the facility will take a minimum of to two to four weeks to complete.