The academy says parents support its policies
The government is planning to close a legal loophole which allows staff at a private Christian academy to smack their pupils.
The Tyndale Academy in east London avoids the ban on corporal punishment in schools by falling outside the legal definition of a private school.
Ministers want to change the law to bring this academy into line.
But Tyndale's founder and principal tutor, Ferris Lindsay, says the government is over-reacting.
Corporal punishment was abolished in all British schools a decade ago. But that ban, and other regulations, only apply to private schools offering a full-time education.
Mr Lindsay says he set up the academy in 1999 to provide part time tuition - just over 16 hours a week - in order to avoid the ban on corporal punishment.
The Christian academy has only eight pupils, but ministers want to use the Education and Skills Bill, currently going through Parliament, to make sure part-time institutions which are the main provider of a child's education also count as schools and have to follow the same rules as other independent schools.
Ministers are concerned that if this academy can legally avoid regulation there may be others in the future who will follow suit.
There is also the possibility that others are operating without the knowledge of the authorities they say.
On its website, the academy, which is based in the Hope Baptist Chapel in Forest Gate, is described as basing its teaching and training on the Bible. It says it welcomes boys and girls from all religious backgrounds.
Mr Lindsay argues that the parents of children at the academy fully support the use of corporal punishment.
He says the policy involves teachers using their hands to smack children on the hand, if they persistently misbehave.
Pupils aged four to seven can receive a single smack; those aged between eight and 11 can be struck a maximum of three times in one go.
According to Mr Lindsay, corporal punishment was used on 12 occasions during the past school year.
Each time parents were informed after the event .
Mr Lindsay described the policy to BBC News as a small part of what goes on at the academy, but said is was so essential to its ethos that if the government did force him to stop using corporal punishment he would close the school.
He alleges ministers are misusing departmental power and resources by pursuing the academy.
According to Mr Lindsay there have been two official consultations, 300 letters or e-mails in one year and now extra legislation.
"That," he told BBC News, "is a sledgehammer to crack a nut."
Schools Minister Jim Knight rejects the claims.
"It is ridiculous to claim that we have singled out Tyndale Academy. We do not make legislation on the basis of one school," he said.
"This is about making sure that parents can be sure their children are getting a safe and secure education wherever they go.
"It is common sense that schools where children receive the majority of their education, unsupervised by parents, should meet minimum standards and be properly registered and inspected.
"No reputable institution should have difficulty complying with statutory requirements."