Answering questions from MSPs about reports that a catalogue of problems at the flagship hospital would cost millions to resolve, Ms Freeman said that was "inaccurate" although there were older buildings on the same site which required upgrading.
However she admitted that there was a "much much higher than acceptable" level of sickness and unfilled posts in domestic and maintenance staff, which would have to be tackled by the NHS Greater Glasgow and Clyde health board to keep on top of hygiene and repairs.
A recent inspection of Scotland's biggest hospital found that some areas could not be cleaned properly because they are awaiting repair work.
The inspection of the Queen Elizabeth University hospital was ordered after patients became infected with a fungus linked to pigeon faeces, and the report found 300 repair jobs were waiting to be done.
Today in Holyrood, Ms Freeman said: "The Queen Elizabeth University Hospital is part of a wider Queen Elizabeth campus which includes older buildings and, as with all estates, maintenance is an ongoing process and the board continues to work through the required maintenance in the older part of the campus.
"The £50m is not a figure recognised by the board because it's not accurate. It doesn't apply to the Queen Elizabeth Hospital or the Royal Hospital for Children, the two new hospitals. The campus has a number of older buildings including neurology, neurosciences, clinical genetics and oncology and the board is working through what the maintenance requirements of those are and where the priority should lie according to which of those buildings which provides patient care."
However Conservative MSP Annie Wells said that while the £50m figure might not have been official despite "it being given by the health boards estates and facilities manager to the corporate management team in January", there was no dubiety about the 300 repairs figure. She asked what the Scottish Government expected the repairs to cost and whether it would have a knock on effect on other patient services.
Ms Freeman added: "In terms of the 300 outstanding jobs, many of those range from what would be basic small scale maintenance which is part and parcel of ongoing maintenance - everything from fixing taps and lightbulbs through to jobs which are about ensuring infection prevention and control.
"The board has produced a detailed plan in response to the inspectorate's unannounced inspection which I commissioned. I have made clear my view of that inspection report, and it's important to put on the record in Parliament that the report was clear that frontline staff were doing all they possibly could to prevent infection and control it where it arose, that they understood their role, and followed the right patient safety protocols, but what was wrong was that issues when they raised them were not being properly heard and addressed.
"So we will continue to monitor very closely what they are doing, and when they produce what they believe to be the maintenance requirement proposals for those older buildings, then that will be part and parcel of the conversation we have with this board. The key, in terms of whether it will affect other areas, is whether or not maintenance required is for patient safety and care in which case priority will be made."
Quizzed by Ms Wells on reports of staff shortages at the hospital, the health secretary said: "It is clear that NHS Greater Glasgow and Clyde carries a higher than acceptable level of unfilled domestic posts there is a much, much higher than acceptable level of sickness absence among domestic staff, it wouldn't be too hard to work out why that might might be the case, and also of maintenance staff.
"Greater Glasgow and Clyde, who are the employers and have to take the action to fill these posts, have had a very clear message from me that I expect them to take that action and fill these posts and we will monitor that very closely."