Freedom of Religion SA (FOR SA) is pleased that the government has heard their pleas for religious leaders and their organisations to be declared "essential workers".
This was after President Cyril Ramaphosa announced that religious gatherings of up to 50 people will be allowed from Monday, with rules.
A national day of prayer and reflection over Covid-19 is also going to be held on Sunday, 31 May.
Freedom of Religion SA (FOR SA) has welcomed the return of religious gatherings from Monday, and the description of religious leaders and congregations as "essential workers".
It said it had sent several letters on behalf of about 18 million people who wanted the government to recognise the "unique contribution" of religious leaders and the organisations.
"In our letters, we also pointed out that many religious organisations have an essential administrative component completely separate from any form of religious gathering.
"These administrative offices/functions need to be able to operate, to continue providing the social relief services (in the form of food distribution and the like) that many religious organisations are actively engaged in during this time."
Churches, synagogues, mosques, temples and other recognised places of worship may also resume services limited to 50 people or less, depending on the space available, and subject to strict health and sanitisation protocols.
"The President's endorsement of the importance of the role of the religious community is significant, and will enable this vital sector of society to be further empowered to help meet the physical, psychological and spiritual needs of our nation in this time of crisis. It is also in line with the earlier decision by Government to re-open the vast majority of the economy in a calibrated way," the group said in a statement.
It advocates for religious rights, regardless of the religion.
FOR SA was most recently in the news for supporting the wedding venue Beloftebos's stance that it would only host weddings between a man and a woman, for religious reasons.
But while FOR SA was excited about group prayer again, the Jesuit Institute South Africa said it was worried about the mixed messages being sent by the government.
"We wholeheartedly support the call for a National Day of Prayer on 31 May, Pentecost Sunday," the institute said in a statement."Many people of faith have suffered the loss and pain of not being allowed to gather in their respective communities for worship. We know this. Refraining from gathering was seen as a way of religious communities actively choosing to care by temporarily stopping a core practice - gathering for worship - for the common good.
"We do not need to open churches right now to practise our faith. Prayer, acts of kindness, reading sacred texts and service of neighbour can continue without gathering in the midst of this pandemic."
It said it found the rushed move questionable, and noted evidence of cluster spreading in other parts of the world suggested that, even if strict social distancing rules were upheld, there were still reports of infection.
"The more people mix, the more there is potential for spread. Places of worship are not immune to the virus," said the institute.
"The government is also sending mixed messages. While a ban on friend and family visits remains in place, it seems illogical that people can gather in places of worship."
The institute said it also created another inequality in a time when inequalities have been highlighted: those who get to attend and those who don't.
"How and by whom will this be decided - and monitored? It goes against the very spirit of being a community of believers to split that community.
"This is an almost impossible decision to make for religious leaders who may have to decide."