The row broke out as it emerged that the number of people who have died with confirmed or suspected Covid-19 in Scotland has hit 4,000.
The National Records of Scotland figures show there were 89 deaths related to Covid-19 registered between June 1 and 7, a decrease of 42 from the previous seven days and the sixth consecutive weekly drop.
As of June 7, there were 1,861 deaths in care homes with the virus mentioned on the death certificate compared to 1,854 fatalities in hospitals. This is much higher than the proportion of care home deaths in England.
It also emerged that more than 700 people in Scotland have been told to self-isolate after being contacted through the Test and Protect scheme.
A total of 681 positive Covid-19 cases were reported, with contact tracing completed for 481. An average of only 1.5 contacts were traced per case, which Ms Freeman said reflected lockdown still being in place.
However, the national care home testing policy has not been delivered in practice at a local level, with the 14 regional health boards moving at different speeds.
The cumulative tests total ranged from 20 conducted by NHS Orkney, where there have been no Covid deaths in care homes, to 2,665 tests run by NHS Lothian, where there have been 409 deaths.
NHS Greater Glasgow and Clyde, where there have been 595 care home Covid deaths, the most in Scotland, had conducted only 920 staff tests.