The source of the infection that contributed to the death of two premature children in the hospital's intensive care unit can never be known, the NHS leader has said.
Babies died after staphylococcus aureus bacteria closing at Princess Royal Maternity Hospital.
The third child in the unit receives treatment after a circulatory infection is closed.
Dr. Alan Mathers said that doctors could never find out what caused the infection.
Dr. Mathers, NHS Greater Glasgow and Clyde Head of Medical, Women and Children, said two dead babies were born very early and were among the "most vulnerable patients" in the country.
But he said that the third child, who also has an infection, "gives us nothing to worry about".
- Two children die after a blood infection
Asked if it was known how the infection began, he told the BBC Good morning Scotland program: "It is not yet and may be that we never come to the root of the problem.
"The issue is that everyone carries the bacteria in their skin and colonizes these things – it is very different from the infection.
"An early child has many systems that are simply not ready for the world, including the immune system, and any violation of the fragility of these babies can lead to bacteria that would not worry us otherwise."
On January 24, an incident management team was established following the detection of a bacterium in a newborn unit.
Staphylococcus aureus is a bacterium found in the skin and nasal tube of about one in four people and causes infection only when it enters the body.
NHS Greater Glasgow and Clyde said in a statement on Wednesday that these three cases are related, and that the dead children were "very bad" because their early childbirth was that infection is one of several reasons for both deaths ".
Dr Mathers said that babies were born so prematurely that there was always a "potential for poor results".
He added: "As far as the intensive care of newborns is concerned, they are the most vulnerable patients on the NHS, stopping completely."
The number of deaths when prosecutors continue to see two deaths at Glasgow's Queen Elizabeth University Hospital. A 10-year-old boy and a 73-year-old woman died of cryptococcal infection.
Jason Leitch, NHS Scotland National Clinical Director, insisted that the healthcare service has effective infection control procedures, although he stressed that it would not be a comfort to those who had lost loved ones.
"These units are safe"
He also said that "there is no better place in the western world" for premature babies to be cared for than Scotland's newborns.
Mr Leitch, also speaking to BBC Radio Scotland, said: "These units are safe and if your child is premature and requires intensive care, it is exactly where you want your child to be.
"There is no better place in the Western world for your early child to take care of intensive care units in Scotland."
Cases of Staphylococcus aureus infection in the NHS Scotland have fallen by 93% over the last 10 years, he added.
Mr Leitch said: "These are rare events, but the fact that they are rare events gives us more opportunities to learn from them and to try to reach zero.
"It would be our hope that Scotland, although it is the world leader in infection control, would be even better."
Analysis by Lisa Summers, BBC Scotland Health Correspondent
Glasgow's worrying health administration is dealing with the third outbreak of infections in a few weeks. Four deaths, two hospitals, two completely separate investigations.
Staphylococcus Aureus is a normal bacterium found on the skin.
It is transmitted through human contact and can also be in the air through skin cells. For most people it stays out of the bloodstream, but it can cause a number of infections if it comes under the skin.
Most of the time you can treat with antibiotics, but it can be serious. Vulnerable very premature babies whose immune system has not developed and need a high level of medical care can be very dangerous if it enters the bloodstream.
The 13-seat Newborn Unit at Princess Royal Maternity Hospital treats very sick and very young children. The question of NHS Greater Glasgow and Clyde here is, is there anything wrong with a rigorous hygiene protocol in a hospital that has created a link between the three cases that have been created?
Queen Elizabeth University Hospital questions about building design and maintenance.
Cryptococcus, a fungal infection associated with pigeon faeces, has somehow penetrated the ventilation system into chapters or sections where additional measures have already been put in place to suppress air quality. They also need to find out how Mucor, another air gas infection, was carried in the hospital.
The Health Board said it was being tracked by a water leak. And once again, how did the bacteria get into the water supply last year, resulting in a number of infants being treated at a children's hospital?
In Scotland hospitals, the total number of infections may decrease, and it is true that infections are a fact of health and can often be dealt with on a regular basis. But there are still many questions to be answered by both the health administration and the government.