Glasgow's NHS board will now be subject to "special measures" following the deaths of two children.
Jeane Freeman said NHS Greater Glasgow and Clyde would be escalated to stage four of the NHS Board Performance Escalation Framework.
But how does the process work?
What are special measures?
Special measures is the term used in England when the existing management of an NHS Trust cannot fix problems without intervention from the government.
Concerns over quality of care or financial issues, and in some cases both, lead to an intervention in which the government takes a direct role in the running of the trust.
According to NHS Providers, the regime was introduced in July 2013 in England when trusts failing to meet adequate standards of quality care were put in special measures.
A similar regime focusing on financial struggles was rolled out in July 2016, with the aim of improving the performance of trusts with unsustainable financial deficits.
There are currently 15 NHS Trusts in England under special measures.
What happens in Scotland?
NHS health boards are not put in special measures, but are instead subject to the NHS Board Performance Escalation Framework.
This scale - from one to five, with five being the worst - determines the performance of a health board and its response.
Health boards can move up and down the scale, and different levels of government support apply to each stage.
Stage one means a board is "on plan" and stage two identifies possible risks if no action is taken.
These stages are policy specific, so a health board could be at stage one in a certain area and stage two in another.
Stage three signifies that risks are materialising and that tailored support is required.
A stage four ranking means there are "significant risks to delivery, quality, financial performance or safety" with "senior level external support required".
Decisions to escalate to stages three and four are taken by the Health and Social Care Management Board (HSCMB).
Ministerial powers of intervention come when a health board is escalated to stage five.
Stage five means that the organisational structure in a health board is prohibiting effective care. The decision to escalate to this level is taken by the health secretary.
How do health boards in Scotland rank?
Five of Scotland's 14 regional NHS boards have already been ranked at level three or above.
NHS Tayside was the last one to be ranked at level five on the scale. That came in 2018 after concerns were raised about the use of funds donated to the health service for IT improvements.
It was claimed the health board used cash from an endowment fund to cover planned expenses, including new computer systems in 2014. NHS Tayside has since improved, and in February this year it was reclassified from a five to a four.
NHS Highland and NHS Borders are also ranked at level four on the performance scale.
NHS Lothian and NHS Ayrshire and Arran are currently at level three.
What happened in NHS Greater Glasgow and Clyde?
There were calls for the government to take greater control over the running of the health board following the deaths of two children.
A three-year-old boy who was being treated for a rare genetic disease died on 9 August 2017. Milly Main, 10, died three weeks later while recovering from leukaemia treatment.
Both children were treated on a ward affected by water contamination at the Royal Hospital for Children, which is part of the Queen Elizabeth University Hospital campus.
Labour MSP Anas Sarwar had called on Ms Freeman to "take control of this situation" and put the health board into "special measures".
In a statement in the Scottish Parliament on Wednesday, the health secretary said she had asked the head of NHS Scotland to review the level of escalation for NHS Greater Glasgow and Clyde "as quickly as is possible".