The Scottish Human Rights Commission is seeking assurances that steps will be taken to address the rising prison population, which has been increasing in recent months.
It is also claimed that incidence levels of the virus among symptomatic inmates are up to six times higher in jails than elsewhere in society.
The Commission is calling for urgent action to better understand the prevalence and increased risks associated with COVID-19 for those who live and work in Scotland’s prisons.
Judith Robertson, Chair of the Commission, said: “Since the start of the COVID-19 pandemic, we have engaged with the Scottish Government and the Scottish Prison Service on a range of issues when it comes to protecting the rights of people who live and work in Scotland's prisons.
"Given the prison population is now rising again, as are COVID infection rates, it is all the more important that action is taken to address our longstanding concerns. In particular, we remain concerned that insufficient data is being provided to enable us to have confidence that people's rights are being adequately respected and protected across the prison estate."
Hundreds of low risk prisoners were released as the scale of the pandemic became clear last year, amid concerns about the impact there would be on an confined environment like a prison in the event of a major outbreak.
But a spokesman for the Scottish Prison service said the impact so far has not been as bad as "we might have feared."
There have only been five Covid-19-related deaths in Scotland's prisons during the course of the pandemic and this is well below the worst case scenarios which was being anticipated.
However, the letter from the Commission states that since the number of prisoners in Scotland's jails has risen again from 6,869 at the end of May last year to 7,465 at the start of this year.
It adds: "Of particular concern is the increase in the remand population. The number of people in prison who have not yet been tried
has increased from 982 in April 2020 to 1,832 on 8 January 2021."
The overall prison population does still remain below the level it was at before the pandemic when numbers stood over 8,200.
The watchdog also raises concerns over the additional restrictions being placed on prisoners who are symptomatic of COVID-19 infection, and those who have been in close contact with them.
"People in prison who do have symptoms may not be identifying as such for fear of those further restrictions," it adds.
"While the reported swab positivity rate for symptomatic persons being tested in the community in Scotland is currently around 10%, information provided to us by the Scottish Prison Service (SPS) indicates that in Scottish prisons on 11 January 2021 that rate was 64%."
This is based on 16 of the 25 persons who were isolated on account of being symptomatic testing positive for the virus.
The letter was also sent to the Scottish Parliament Justice Committee and Her Majesty's Chief Inspector of Prisons in Scotland.