The review into a Glasgow hospital where two people died after contracting an infection is expected to report back with its findings in spring of next year.
An independent investigation was announced following an infection outbreak at the Queen Elizabeth University Hospital (QEUH) earlier this year.
The infection contracted by the two people who died is thought to have been related to pigeon droppings.
Speaking at the Scottish Parliament on Wednesday, Jeane Freeman said she expects the review to “fully address and investigate all matters it considers relevant” to its investigation.
Ms Freeman said it would include looking at the building’s design, commissioning and construction, handover and ongoing maintenance at the QEUH.
The Health Secretary said the co-chairs of the inquiry have started to review documentation and have been consulting experts from various fields in order to appoint the review panel.
The terms of reference have also been produced and will now be discussed with stakeholders, the Health Secretary said.
Ms Freeman said: “The co-chairs have reviewed a considerable amount of documentation and consulted extensively.
“They have also sought advice from experts from different fields with the aim of appointing individuals to the Independent Review Panel or asking them to lead advisory work-streams as part of the review process.
“As a result of their work so far, the co-chairs have drafted terms of reference for the review, and intend to ask stakeholders for their feedback to ensure that the review remains correctly focused.
“It is essential that those affected by the issues examined by the independent review have the opportunity to have their views heard.
“The co-chairs therefore welcome communications on the matters being considered by the review.”
She added: “As the review progresses, regular updates will be provided and, where significant findings emerge, these will be reported and acted on promptly.
“The review must remain flexible to accommodate valuable contributions in order to produce a thorough, searching review of all key events and issues at stake, and to make recommendations to ensure that NHS Scotland facilities are fit for purpose and support the delivery of world class health care.”
Earlier on Wednesday, MSPs wrote to Ms Freeman to seek greater clarity on the probe.
Holyrood’s Health and Sport Committee has carried out its own inquiry into healthcare environments across Scotland but its convener, Lewis Macdonald, said the Government must provide further information on the probe.
He said: “Our inquiry into healthcare environments across Scotland raised a number of concerns and, while the Cabinet Secretary was able to address some of those in her response, more information is needed.
“There are areas, particularly around the independent inquiry into Queen Elizabeth University Hospital, where the Government must provide more clarity.
“It’s vital that people have faith in the independent process of an inquiry and that it is as comprehensive as possible so that lessons can be learned from the recent incidents at QUEH.”