The Church of Scotland - with 1400 congregations - raised more than £108million and six of the eight Catholic dioceses brought in more than £38million.
The figures are available for the first time after a shake-up in charity laws. Figures for other religions will be released later.
The Office of the Scottish Charity Regulator (OSCR) granted "designated religious charities" status to the organisations in October, including the Free Church of Scotland and the United Free Church of Scotland.
Much of the income comes from the pockets of church-goers.
But the churches also generate cash from vast property portfolios, legacies and social care work.
Niall Cooper, of Church Action On Poverty, said: "It will be a startling figure for many people and it shows the generosity of the Scots."
The Kirk is among 19 of Scotland's 23,500 registered charities to raise more than £100million a year.
A Kirk spokeswoman said: "The gross income is not profit. It is money that came in during 2006 but of that £46.3million came from offerings.
"We have legacies, charitable works and all manner of other things that bring in the rest."
The Sunday Mail has also learned how much income each of the Catholic Church's eight Scottish diocese raised.
The total income from its 500 churches was more than £38million but the church refuses to say how much is raised in Sunday collections.
Glasgow diocese generated most - almost £13million - and Aberdeen the least, around £700,000.
ACatholic spokeswoman said: "It may seem a lot but it gets put to a lot of good uses."
The Free Church of Scotland, known as the Wee Frees, recorded a 2006 income of almost £6million.
The tiny United Free Church pulled in more than £1million.
The income from all the churches does not include valuable fixed assets such as property.
Tax expert Valerie Smart, of PricewaterhouseCoopers, said: "Until 2005, when the new Scottish Charities Act came in, the Inland Revenue dictated who could become a charity.
"The Act broadened the definitions of a charity to include lifesaving, arts and heritage societies.
"Some of the religious charities are among the biggest in the UK.
"The mainstream religious bodies have been around for a very long time.
"They were working to relieve poverty and ease bad health long before the NHS. They have a long history with communities and that's why they are able to raise so much.
They are intertwined in our social fabric and vital to the economy."
The charity regulator said: "Designated religious charities are those which have applied to OSCR and been granted this status.
"It exempts them from certain requirements as they are deemed to have sufficient internal reporting and disciplinary structures."
THE CHURCH RICH LIST
Scottish income for 2006:
CHURCH OF SCOTLAND £108,342,000
RC CHURCH £38,150,828
(Glasgow: £12.8m; Dunkeld: £8.4m; St Andrews & Edinburgh £7.7m; Galloway: £3.5m; Motherwell £2m; Paisley £1.6m; Argyll & Isles £1.2m; Aberdeen £713,179)
FREE CHURCH OF SCOTLAND £5,744,863
UNITED FREE CHURCH OF SCOTLAND £1,080,713
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