Experts in human rights law have accused the Irish government of lacking transparency and accountability in key decision-making during the pandemic.
A report by academics from Trinity College Dublin said there was a lack of clarity about how decisions affecting prisoners and asylum seekers were made.
It questioned how policies were arrived at in the vaccination programme and how Covid-19 deaths are counted.
The report also said it was unclear who made some key decisions.
The Trinity academics said there was a lack of transparency over whether some Covid-19 measures were legally enforceable.
The report echoes many criticisms already made by some opposition politicians about the relationship between the government and members of the National Public Health Emergency Team (NPHET).
Sarah Hamill, an assistant professor of law at Trinity College Dublin, said: "If we don't have clear lines of decision-making and accountability, and a clear sense of the power resting with the government, then the idea that we can have even notional democratic oversight for these powers seems very remote.
"This is undoubtedly a cause for concern."
She and her team have made 16 recommendations, including clarifying the relationship between ministers and NPHET.
They also said the prison service should make public in a timely fashion the measures they are adopting to deal with the pandemic.
They found prisoners were affected by reduced visits and more limited access to showers because of Covid-19 and this posed human rights challenges.
The Trinity academics made similar findings in the cases of asylum seekers in Ireland's direct provision system.
Asylum seekers are accommodated in centres run by private companies until their applications for protection are heard.
The system has been widely criticised because of the poor conditions many live in and the Irish government has pledged to wind it down and replace it with something better.
The human rights experts also argued the current law may allow employers to impose a vaccine requirement on workers because of the "exceptional circumstances" of the pandemic.
Such a development requires "rigorous justification and careful planning to take account of specific factors that may affect individual employees", they added.
The Trinity academics also found the Republic of Ireland's method of calculating Covid deaths is too often "too lenient with respect to time periods" giving false impressions at times as to how widespread and deadly the virus is.
The Irish government has yet to give its response to the academic findings but in the past it has rejected similar conclusions arguing that it has had to deal with an evolving pandemic situation and take the necessary measures to stop the spread of the virus.