Pigeons were dismissed as a nuisance just months before two patients died from an illness linked to their droppings.
NHS Greater Glasgow and Clyde were warned over fears of contamination infections from the birds at Queen Elizabeth University, The Sunday Mail reports.
The NHS board claimed its public health consultant deemed the problem an "environmental nuisance rather than major risk for human health”.
Documents reportedly revealed "there is no specific policy" to protect the public from contracting diseases linked to pigeon droppings.
Prosecutors are investigating two deaths at the hospital, that of a 10-year-old boy in December 2018 and a 73-year-old woman in January of last year.
Both incidents have been linked to cryptococcus infections from pigeon droppings.
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The plant room, which was initially thought to be the source of the infection, has been ruled out in the 12 months since the board announced the investigation.
And a probe has so far been unable to locate a source.
The Glasgow hospital has had a string of problems since its opening in May 2015 leading to an improvement notice issued by the Health and Safety Executive.
It has also been criticised for the deaths of two children who were treated on a ward affected by water contamination.
Three-year-old Mason Djemat and ten-year-old Milly Main were treated at the Royal Hospital for Children within the campus at the time.
READ MORE: Mother of tragic Milly Main demands fatal accident inquiry into her death at Glasgow super hospital
It has been alleged a doctor-led probe at the QEUH found 26 cases of child cancer patients acquiring water infections in 2017.
Health Secretary Jeane Freeman was forced to launch a major review of the design of the facility last year.
Monica Lennon, Labour’s shadow health spokeswoman, said: “Scotland’s flagship hospital has been rocked by scandal after scandal and the link between patient deaths and pigeon droppings sent shockwaves around the world. These tragedies should never have happened.
“The people of Scotland need to know that our NHS is in safe hands. It’s becoming clearer by the day that bosses at NHS Greater Glasgow and Clyde have lost the confidence of the public.
“Jeane Freeman appears to be the only person in Scotland who is happy to let the chief executive and the senior leadership team carry on. Our NHS must be in safe hands.”
Conservative shadow health secretary Miles Briggs added: “Clearly the pigeons at this flagship hospital were anything but harmless.
“This reveals a real complacency at the heart of the health board and the SNP Government about the safety of patients and staff.”
The health board denied there was any risk to patients from pigeons in its response to a freedom of information request submitted by a member of the public in March 2018.
In response, NHSGGC said: “The situation with the pigeons is continually monitored by NHSGGC and we are proactive in our efforts to reduce the problem.
"However, we have sought comments from our consultant in public health with special responsibility for environmental concerns who has advised us that, in general, the risk for health posed by exposure to these pests is considered to be relatively minor.
“We are aware that this particular issue concerns a hospital and a population of potentially vulnerable patients rather than residential or commercial premises, but an infestation of this kind would normally be considered as an environmental nuisance rather than a major risk for human health.”
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A spokeswoman for NHSGGC said: “Our thoughts and sympathies remain with the families of two patients who were treated for a Cryptococcus infection and sadly later died.
"The safety of our patients is at the centre of everything we do and we encourage any family with any question or concern to speak to a member of staff so that this can be responded to personally.
"In the 12 months since we announced an investigation into the two cases, we have continued to work with international and national experts to examine a number of potential hypotheses about a possible source of the Cryptococcus fungus (neoformans).
"To date this expert panel has identified; as Cryptococcal fungi are widespread naturally occurring in the environment - a specific source has not been found, no evidence of Cryptococcus neoformans in or around the hospital, the plant room – initially thought to be the source – has been ruled out, there have been no further cases since last year."
They added: "Our public health team with special responsibility for environmental concerns has confirmed that the risk to healthy humans from pigeons is low.
"For those who are vulnerable to infection from environmental bacteria or fungi because of their illness or treatment, NHSGGC have clinical protocols to protect them from infection – including the option to place patients in facilities with specialist ventilation and treatment with a range of prophylaxis antibiotics and antifungals.
They added: "Our public health team with special responsibility for environmental concerns has confirmed that the risk to healthy humans from pigeons is low.
"For those who are vulnerable to infection from environmental bacteria or fungi because of their illness or treatment, NHSGGC have clinical protocols to protect them from infection – including the option to place patients in facilities with specialist ventilation and treatment with a range of prophylaxis antibiotics and antifungals.
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