He said the review painted a picture of a ministry short on support needed to provide stronger leadership and governance of the health sector.
"Many of the issues highlighted in this report were also identified in the 2012 PIF Review. It's clear things were going from bad to worse under the previous Government," said Clark.
"We need a strong, stable and high-performing ministry leading our health and disability sector. The challenge for the ministry's new leadership will be to deliver just that."
He said it was vital the ministry rebuilt trust and confidence in itself so that it could deliver on the Government's health priorities, including making primary healthcare more affordable and accessible.
Jonathan Coleman, the former Health Minister and National's health spokesman, said he did not agree with all parts of the SSC report, such as the description of the weak leadership.
"I actually think they've got some excellent leaders in the Ministry of Health. It's a very challenging ministry and a $17 billion budget. It's a portfolio that touches everyone in New Zealand, everyone has got an opinion about it.
There's always been tension between the Ministry of Health and the sector. These are tough challenges and I think Dr Clark is about to find out just how tough the portfolio really is."
He said Clark had made a lot of promises prior to the election and now had to deliver.
The review said the ministry's challenge was to use its stewardship role to lead the health and disability system and improve lifetime health and well-being of all New Zealanders.
Given current disparities in health outcomes and well-being, the ministry had to focus on improving access to health services for the youngest and oldest who fared the worst in health statistics.
In response the ministry said it would focus on better directing investment to address inequity and improve people's lives.
Director-General of Health Chai Chuah said a key challenge would be to change the ministry's current healthcare mindset from illness to health and well-being, which encompassed a whole person's life and involved family in support.
Plans were under way to develop a national electronic health record which would be accessible to health providers through a patient portal network.
The new system would allow for a strong outcome focus for patients and allow for better information sharing across key sectors.
It is one of two reports released today with the second expected to also be critical of the ministry.
This afternoon the second stage of a Government inquiry into the drinking water contamination that caused an outbreak of water-borne disease in Havelock North, which saw almost half the town's population become ill, will be released.
Earlier this week the Chuah announced he would stand down halfway into his five-year term, while Clark set up an urgent Ministerial Advisory Group on the health system, saying "all is not well".
