Health boards collectively spend about £3.7m a year on the internal departments, including paying salaries of full-time "generic" NHS chaplains who are tasked with providing support to all who ask for it.
In addition, the NHS has made payments of almost £600,000 to churches to attend to the religious needs of individual patients in the past three years, figures obtained by The Herald under Freedom of Information laws revealed.
More than 85% of spending on the external bodies went to the Roman Catholic Church, largely in exchange for priests to come in to hospitals and perform sacraments such as the last rites, which NHS chaplains are not able to carry out.
Scotland's largest health board, NHS Greater Glasgow and Clyde, said its in-house chaplaincy department was allocated a budget of £632,665 in 2013/14, with the service "providing non-denominational support to our 38,000 staff and all our patients".
It also pays £75,000 per year to the Archdiocese of Glasgow and the Diocese of Paisley in exchange for "on-call" priests, "to provide the Sacramental ministry that Roman Catholic patients and families expect".
It previously also paid money to the Church of Scotland and the Episcopal Church, before the arrangements ended after March 2012.
Spencer Fildes, chairman of the Scottish Secular Society, called for payments to external churches to be scrapped and for budgets for internal chaplaincy services to be re-examined urgently.
"We believe chaplaincy services are essential, but we don't support their funding by the NHS," he said. "The cost of £3.7m a year is quite astonishing, particularly when frontline services are being cut and there's a desperate need for more healthcare professionals across the country.
So what do you think? Should the NHS be funding religious organisations to provide for the spiritual needs of the patients in their care or should this be left in the realm of the churches, etc?
My view is that this should be paid for by the relevant religious bodies in the local area. They're expected to attend to their congregations in the community without requiring bribes to do it and it's shameful that they require these payments should someone cross the threshold of a hospital.