Ms Freeman said "exceptional circumstances” could allow Covid-19 positive patients to be sent to homes from hospital if a “clinical decision” deemed it necessary.
However her comments on BBC Scotland saw her accused of failing to learn from the first wave of coronavirus which saw thousands of elderly people die in Scottish care homes.
Scottish Conservative shadow health spokesman, Donald Cameron, said: “The SNP has clearly not learned the harsh lessons of the first wave of the pandemic, when we saw Covid-19 ripping through care homes if given even the slightest chance.
“This is exactly why we needed an immediate public inquiry on what happened in our care homes, and it’s out of order that the SNP still won’t launch that inquiry.
“If this practice is allowed to happen again, it has the potential to be a disaster that ends in the tragic loss of even more lives. This isn’t about challenging clinical decisions, it’s about the reckless message being sent from the health secretary that it could be “entirely right and proper” to discharge patients without a test.”
The Scottish Government has repeatedly come under fire for the handling of care homes during the pandemic. Its current policy states that two negative tests are needed for a patient who was being treated for Covid-19 to be discharged into a care home and one negative test if they were dealing with another ailment.
However, should a discharge be deemed necessary by clinicians, a patient can be moved out of hospital, Ms Freeman said today – though this would only occur in “exceptional circumstances”.
In an answer to a parliamentary question from Labour health spokeswoman Monica Lennon, reported by the Sunday Mail, the Health Secretary said the discharge should only be allowed if “it is in the clinical interests of the person to be moved”.
On Sunday she said the final decision would be made by health and social work professionals, adding it would not be appropriate for politicians to intervene.
She said: “If and where older people are being discharged from hospital into a care home or back into their own home without the two negative tests for coronavirus that we have in our policy position, that will be a clinical decision made by a clinical team and the social work team that are working with that elderly person and their family.
“It is entirely right and proper, I think, that clinicians who are experienced in elderly care and medical care and social work staff experienced in social work support for older people are the ones who will make the final decision.
“It is not right, and I don't believe your viewers would expect, me as a non-medical, non-clinical politician to be intervening in that decision.”
She added: “The care homes themselves take serious responsibility about their infection prevention and control procedures, and do their very, very best to follow our guidance, with our support, on PPE and other matters.”
A report released last month by Public Health Scotland found more than 100 people were discharged from hospital to care homes in the early part of the pandemic without first testing negative for coronavirus.
Ms Lennon said: “People known to have Covid-19 should not be placed in care homes and Jeane Freeman must put a stop to this dangerous practice immediately before more lives are lost.
“Thousands of older and disabled people living in care homes have been forbidden from even talking to their loved one through the window, yet the Scottish Government is allowing residents to bring the virus through the back door.
“Too many lives have already been sacrificed. This must end today."