US Edition In his Easter sermon, he warned that it was the “worst possible moment” to lower the status of the subject amid concerns over a rise in the influence of aggressive secularism.
Dr Williams said children’s hostility towards religion was not as extreme as society perceived, with many taking the issue of faith seriously.
The comments come just weeks after a major report from the Church of England warned that pupils’ moral and spiritual development risked being “pushed to the side” because of Government reforms that put an increasing focus on the teaching of the three-Rs at the expense of many other subjects.
According to one study, the number of schools teaching RE to a good standard in the state system has dropped sharply in the last 12 months.
Speaking at Canterbury Cathedral, Dr Williams said: "There is plenty to suggest that younger people, while still statistically deeply unlikely to be churchgoers, don't have the hostility to faith that one might expect, but at least share some sense that there is something here to take seriously - when they have a chance to learn about it.
"It is about the worst possible moment to downgrade the status and professional excellence of religious education in secondary schools – but that's another sermon."
Last month, a study by the C of E claimed that religious education was being undermined by a series of Coalition reforms.
It criticised a decision to exclude RE from the English Baccalaureate – a new school leaving certificate that rewards pupils gaining good grades in five core academic disciplines, including maths, English and science.
The Church also highlighted a decline in the number of new RE teachers being trained and a refusal to include the subject from a major review of the National Curriculum, which will set out the key facts pupils should learn at each age.
According to a separate study, some 24 per cent of comprehensives and 31 per cent of grammar schools failed to offer the subject to 14- to 16-year-olds last year. Fewer pupils are also being entered for full GCSEs in religious studies.
The research – by the National Association of Teachers of RE – warned that this “non-compliance” was expected to increase in the current academic year.
In his final Easter sermon before standing down as head of the Church, Dr Williams said that hostility towards faith and religion may have been tempered by a recent appreciation of the social value of religion.
But he insisted that the ultimate test of Christianity was not whether it was beneficial to the human race but whether the resurrection of Jesus Christ actually happened.
In his Easter Sunday sermon, Cardinal O'Brien, leader of the Roman Catholic Church in Scotland, told worshippers to "wear proudly a symbol of the cross of Christ" each day of their lives.
He was also voiced concern at the growing "marginalisation" of religion.