ScotCen, found 58 per cent of respondents said they had no religion at all, compared with 40 per cent when the survey was carried out in 1999.
The Church of Scotland saw the sharpest decline, with just 18 per cent saying they belong to the Kirk. That figure stood at 35 per cent in 1999.
ScotCen researcher Ian Montagu said: "The decline in religious identity in Scotland has been most keenly felt by the Kirk as fewer and fewer people choose to describe themselves as Church of Scotland by default.
"As each generation coming through is consistently less religious than the last, it is hard to imagine this trend coming to a halt in the near future."
The proportion of Roman Catholics and other Christian affiliations in Scotland has remained relatively stable over the same period.
Montagu believes the Church of Scotland needs to make changes to reverse the declining figures. He added: "If the Kirk is able to push through liberalising measures such as allowing ministers to oversee same-sex marriage ceremonies, it is possible that its appeal may broaden somewhat to younger, more socially liberal Scots."
Rev Norman Smith, the convener of the Church of Scotland's Mission and Discipleship Council, told the BBC: "This survey contains no surprises for us a Church, however for us it is only part of the story.
"Other surveys such as that reported recently in the Daily Telegraph show that Christianity continues to have an impact on people's lives."
The news agency had previously reported new figures show that one in six young people are practising Christians and research suggests thousands convert after visiting church buildings.
Rev Smith went on to say: "The challenge for us then as Church is to find ways that connect people's everyday life to faith. We recognise the Church needs to develop new ways of communicating a faith that we believe is still relevant to life in the 21st century."
The survey interviewed a representative random probability sample of 1,237 people between July and December 2016.