The public health watchdog announced the change in policy on Wednesday in its most recent Covid-19 statistical report, saying the frequency and content of the data would be reviewed.
Instead, officials will focus on publishing more robust and complex vaccine effectiveness data.
Significant concerns about the data being misused deliberately by anti-vaccination campaigners is behind the move, PHS officials told The Scotsman.
The report published on Wednesday will be the last weekly publication to include the data which includes information on Covid-19 infection rates among the vaccinated and unvaccinated, as well as hospitalisation and death rates, broken down by the number of doses received.
Officials said that two central issues relating to the unvaccinated population and testing habits meant the data was no longer reliable or robust and open for misinterpretation without adequate context.
This is due to the fact that the population data used for the unvaccinated population is based on GP registration details, meaning it includes thousands of individuals who are registered but may no longer live in Scotland or simply failed to deregister.
As the vaccinated population grows, this flaw in the data becomes more pronounced due to the true number of unvaccinated people being much lower than the number used, making the final published data less reliable.
Vaccinated people are also more likely to report the results of lateral flow tests, further skewing the data due to changes in how a test result is formally recorded with individuals no longer needing a PCR test to confirm infection.
One PHS official said that focusing on vaccine effectiveness rather than the existing “very simple statistics” would result in “much more robust” data for the public.
They said: “The main important point around all of the analysis is we understand whether the vaccines are working against catching it and against getting severe Covid, and that’s where the vaccine effectiveness studies come in which are a completely different methodology.
"The case rates, hospitalisation rates, the death rates are very simple statistics, whereas for the vaccine effectiveness studies we use modelling, we compare people who have tested negative to those who have tested positive and match them on their underlining co-morbidities.
"It’s a completely different method which is much more robust and that’s what we want people to focus on.”
The data has been promoted on social media by individuals including The Spectator’s associate editor Toby Young, the American right-wing opinion website, The Blaze, and anti-vaxxer American talking head Alex Berenson.
The PHS official added: “What is happening is people are looking at those simple data and trying to make inferences about the vaccination, whether the vaccines work, inappropriately and sometimes wilfully.
"There are so many caveats and they just pull certain figures out that should not be used.
"What we are going to do is do a lot more on the vaccine effectiveness side and try and make people understand how effective the vaccine is.
“For example we know it is 50 per cent effective against getting infected, but that it is much higher effectiveness against hospitalisations and deaths which is the key thing really as that’s what we want to prevent.”