Ministers are reminding England's local authorities that, by law, they should not be closing rural schools.
Proposed closures often provoke a strong local reaction
A letter is being sent to all councils - amid a public lobbying campaign aimed at stopping small school closures.
The Liberal Democrats accused the government of muddle and hypocrisy because of guidance it has also issued saying surplus places must be closed.
The Tories say many small schools have gone in the past decade despite Labour's promise to protect them.
A fall in the birth rate some years ago has meant there are fewer children of school age.
The Liberal Democrat spokesman David Laws said: "Today the schools minister is telling everyone that the closure of smaller schools is not on the government's agenda.
"However, government guidance issued to local authorities just one month ago makes clear that ministers expect local authorities to close smaller schools and remove surplus places as a 'priority'."
What this Primary Strategy for Change document says is that the Department for Children, Schools and Families expects to see decisive plans for early action to ensure that no school has more than 25% surplus places and to reduce overall surplus places to less than 10% in each area.
However it also says: "It will not always be practicable, or desirable, to remove all surplus places."
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Authorities should allow for parental choice, among other things.
Small village schools are much more part of the community than large schools
"It is also accepted that in order to preserve access for young children, there may be more empty places in schools in rural areas than in urban areas," the guidance says.
Mr Laws said local authorities were being told that unless they followed the government's blueprint, they would not get the money for new or refurbished primary schools.
Schools Minister Jim Knight's letter to councils tells them they must take very seriously the statutory requirement in the 2006 Education Act that there is a presumption that rural schools will not close.
Mr Knight said: "This is not about funding. This is caused by falling birth rates coupled with families moving from rural to urban areas, which leaves some communities with falling numbers of pupils.
"Closing schools is a drastic last resort for councils.
"It's unacceptable for them to propose closing popular, successful schools which parents want to send their children to, if they have not fully looked at alternative uses or consulted their communities."
Alternatives included federating schools under one leadership team or housing other services in their buildings, such as playgroups.
Officials at his department said primary pupil numbers had fallen by about 10% since 1999.
Closures of rural schools increased in the 1970s to a peak of 127 in 1983, continuing at around 30 a year up to 1997.
In February 1998, the government had put in place a presumption against the closure of rural primary schools.
They say that since then, the rate of closures has been reduced from an average of 30 a year to seven.
Official figures obtained by the Conservatives show that since 1997 the number of secondary schools with under 600 pupils has declined by 42% from 904 to 526.
The number of primary schools with fewer than 100 pupils has fallen by 219 (8%) to 2,605.
Shadow children's secretary Michael Gove said: "Back in 1998 Labour pledged to save small schools, but these figures tell a very different story."
He said ministers were trying to shift the blame onto local authorities even though it was government rules that were contributing to the problem.
"We will change those rules so that good small schools can prosper and more new ones can open."
Figures on empty places also show a reduction of 386 in the total number of primary schools in England of all sizes between 2006 and 2007.
A spokesman for the DCSF said: "It is simply wrong to claim that our guidance to local authorities is 'misleading'. It is nonsense to say we have told local authorities to close up to one in 20 schools.
"Our guidance makes it clear that we want local authorities, as part of their plans to improve primary school buildings, to target the 5% of schools in the worst physical condition and rebuild them or take them out of commission."