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.
