If churchgoing is a reliable indicator of Christian belief, then England began losing its religious impulse when Victoria was still on the throne. Attendance at Anglican services began its decline in the 1890s. By 1968, only 3.5% of the English population went regularly on a Sunday. By 1999, that figure had halved to 1.9%. And, as the numbers went down, the age of the congregations went up. The average age of a member of the Church of England is 50. In 2015, it is likely to be 55. If present trends continue – a phrase, admittedly, that always invites suspicion – then in 30 years' time two thirds of observing Anglicans will be more than 65 years old, and almost all of them will be women.
The social, constitutional and moral consequences of the church's shrinking importance are often debated, but perhaps the real threat, which all of us can care about, is aesthetic. More numbers: three quarters of England's 16,000 parish churches are listed as buildings of architectural and historic interest in Grades I, II* and II. Churches listed grade I comprise 45% of all England's buildings – castles, mansions, banks, railway stations, markets – in the same first rank. In the words of an official from English Heritage, this means that less than 2% of England's population is directly responsible for the care of nearly half of England's finest architecture.
Public funds have helped the churchgoers. Since 2002, English Heritage and the Heritage Lottery Fund have spent £179m on repairs to listed places of worship of all denominations (but mainly Anglican), and every year another £12m is doled out in grants equivalent to the VAT paid on the work. The fear, for English Heritage and the church, is that a Treasury hungry for cuts won't renew the VAT scheme when it runs out next year. In a report this week, English Heritage reckons that only about one in 10 listed places of worship is in poor condition, but implies that if the cuts come this number will grow. More leaking roofs, more broken stained glass, and then ruin or conversion into flats.
Lincolnshire is a good place to consider these things. "The second largest county in England and the least appreciated," John Betjeman wrote in his Guide to English Parish Churches. The Lincolnshire wool trade, flourishing in the 12th to 15th centuries, left behind a fine stock of medieval naves, chancels, windows and towers; Lincolnshire has 913 buildings listed Grades I and II* and 418 of them were built to be prayed in. Like other rural counties – Herefordshire, Rutland – it has an unusually high number of listed churches per head of population. "A pre-industrial legacy," in the words of this week's report, "means that the cost of maintaining buildings falls to a disproportionately small number of people, mainly in rural areas."
And so it does. Here we are on a lovely morning in Beckingham, near Newark, looking at the Norman architecture of All Saints (Grade I) with the churchwarden, Gill Green, a lively woman who walks with a stick. Some parts of All Saints date from the 12th century and other parts from the 13th to 15th, but all of it was restored in the 19th. The 20th was less kind. Gill Green says that one of its vicars, now dead, took more interest in selling off the glebe land than in the fabric of his church. Feckless vicars often carry the blame for ruination – "There are no problem buildings, just problem owners," says Dale Dishon of English Heritage – but the brutal facts have to be faced. Two hundred people live in Beckingham, a mere nine of whom sit in All Saints at a regular service. The Lincoln diocese tried to make it redundant as a church 10 years ago, but Green and others in the tiny congregation organised a campaign and English Heritage offered a grant for repairs. A rural dean takes services here, a duty he shares with four other churches, all Grade I, but the pipe organ has gone, the tower is unclimbable, the bells untollable, the steam heating broken. Cold keeps the church closed in winter and even in summer damp plaster crumbles at a touch.
A grant has bought a new roof, but other repairs or restorations (of the tower's crocketed pinnacles, say) will need to be funded in other ways. Poverty is forcing churches to open up to the material and secular world, aka "the wider community", partly because state subsidies encourage them in that direction but also because many local people who have never and will never step inside one for religious reasons still see them as important and often beautiful landmarks that give a place a history. These people give just as generously as Anglicans to fundraising projects.
For this reason the phrase "tea point" appears in English Heritage's guidebook for fundseekers. At All Saints they plan to put the tea (and coffee) points, the sink and the toilets at the western end of the nave, just under the tower. Then, in a village without a shop or a school, the church could have all kinds of uses – meetings, talks, and playgroups as well as worship – that would give it a more practical value to the parish. Green's big concern, she says, is "to keep the church going somehow for the glory of God. I'd hate to be the last person who locked the door of a building that has witnessed continuous worship for 900 years".
In Benington, a village of 450 people near Boston, I heard the same: that it was inconceivable to lose a building (another All Saints, Grade I) that for 900 years had provided generation after generation spiritual consolation and pastoral care. In fact, All Saints Benington closed as a church in 2001, but thanks to the work of an enthusiastic local committee it has since been restored as a building for community use where services are permitted six times a year. Many institutions chipped in with money and advice – including English Heritage, the diocese, and the Churches Conservation Trust, a charity funded by the state and the Church Commissioners that looks after churches put to other uses (one has a swimming pool in the nave).
Finally, we drove through the Wolds to Raithby-by-Slingsby, where English Heritage is spending £350,000 on repairs to Holy Trinity: a dark and romantic little church, Grade I, 12th century, extravagantly restored and decorated by a succession of Victorians beginning with George Gilbert Scott in 1873. How many people live in Raithby? About 170. Where is the next nearest Anglican church? About a mile away. Canon Peter Coates, who met us at the lych gate, said this was an area particularly rich in churches – 41 consecrated Anglican buildings and four priests served a population of 10,000. The canon had seven active congregations and one redundant parish under his charge, and it would be fair to assume that some if not all are among the hundreds of Anglican churches that can muster a regular Sunday attendance of no more than 10.
Nothing as handsome as these churches will ever again be built in these villages; their presence there seems almost miraculous, like finding an original Leonardo in a Skegness postcard rack. But how empty they are! Christian worship seems to have melted away almost as completely as the wool trade, and long before Richard Dawkins and the atheist revival came hunting for an argument. We should at least take care to preserve its inspiring remains.
• This article was amended on 5 July 2010. The original referred to medieval knaves, chancels, windows and towers. This has been corrected.