In an open letter to the First Minister, the group of leaders claim there is no evidence churches have led to the spread of the virus and suggest closing them is “unlawful”.
They go on to accuse the Scottish Government of “failing” to understand that Christian worship is an “essential public service”.
The letter says: “We understand entirely the exceptional difficulties of leading the country at the present time and we and our churches have prayed for wisdom and clarity for your government repeatedly.
“But we strongly disagree with the decision to prevent the gathering of the Church at this time, which we believe is profoundly unhelpful and may be unlawful.
“We know of no evidence of any tangible contribution to community transmission through churches in Scotland. To the contrary, since churches re-opened in July we have demonstrated that places of worship and public worship can be made safe from Covid transmission.
“However, above all we are dismayed because there seems to be a failure in the Scottish Government to understand that Christian worship is an essential public service, and especially vital to our nation in a time of crisis.”
Churches have remained open in the rest of the UK and the group has now accused the First Minister and Scottish executive of “disadvantaging” the people of Scotland.
The letter continues: “The United Kingdom Government has rightly heeded these important and persuasive arguments and has since, even in the face of a national lockdown, preserved this essential contribution to the wellbeing of the nation by allowing public worship to continue in England.
“We urge you not to disadvantage the people of Scotland by failing to recognise both the moral and legal arguments for the priority of public worship, and also the weight of scientific evidence for its essential contribution to the public good.
“We urge you not to be the government which denies our nation the collective prayer of the churches of our land in days when it is most greatly needed.
“We echo the words of the Archbishop and other leaders to the Prime Minister and call on Scottish Government to recognise and support this, and enable us to continue to worship safely as part of the essential fabric of the nation."
The main authors of the letter include Rev Dr William J U Philip from the Tron Church in Glasgow, Rev Paul Ree, a Senior Pastor, at Charlotte Chapel in Edinburgh, and Rev John Mackinnon, a Senior Pastor at Calderwood Baptist Church in East Kilbride.
Along with the 200 leaders in Scotland, the letter was also signed by another 300 from England, Wales and Northern Ireland.
A Scottish Government spokesperson said: “We know how tough this decision will be for many people. However we must take action across society to stop the virus spreading further, so we can protect public health and save lives.
“The virus transmits when people come together and therefore we have to reduce, as far as possible, the places where they do so – this involves the decision on places of worship, just as it does schools, and workplaces so we can keep the country as safe as possible.