The Royal Hospital for Children and Young People in Edinburgh was due to open last month, but was halted after final checks revealed the critical care unit’s ventilation system did not meet the necessary standards.
Ms Freeman said on 18 July that water and drainage systems at the site would also be assessed before a timeframe for the transfer of patients could be established.
A union official has suggested drainage issues have led to concerns the building may have to be “ripped down”.
Labour has called for Ms Freeman to resign.
Asked about drainage problems on BBC Radio Scotland yesterday, Ms Freeman said: “I have asked for a number of other critical areas of the existing new hospital site to be double checked to make sure they are compliant with all standards and that will include drainage.”
The health secretary added: “As far as both those involved in addressing the issue and the board are concerned, the issue has been resolved.
“But I have asked for those additional checks, along with others – not just on drainage – to be made so I can be sure that every aspect of that hospital that relates to patient safety and staff safety, that I have the additional assurance that they are all compliant with the relevant standards.”
It has emerged NHS Lothian is handing over around £1.4 million a month to hospital developers Integrated Health Solutions Lothian (IHSL) despite the fact it is not yet operational.
KPMG is carrying out an investigation into the delays, while Scottish Labour has called for a public inquiry.
Ms Freeman said: “I’ve been very careful to make sure local MSPs and MPs are kept informed with everything I have done so far and I will inform them as the information becomes available.
“For the Health and Sport Committee of the Parliament, it is of course entirely up to them how they want to
proceed on any matter, but I will co-operate with whatever they decide, as I always have done.”
A Scottish Government spokesman said: “The Health Secretary has been clear her first priority is patient safety and all necessary actions are taken to allow the move to go ahead as quickly and safely as possible.
“In addition, the Health Secretary has confirmed KPMG have been engaged to conduct an independent audit.”