Bible-based centre practising corporal punishment will be brought into line.
Ministers hope a private Christian academy that still uses corporal punishment can be brought into line by creating a new legal category of educational institution.
At Tyndale Academy in Forest Gate, east London, where rules are based on the Bible and pupils aged 5 to 13 can be smacked on the palm with a teacher's hand for direct disobedience, or acts they know are wrong, such as persistent swearing.
All school staff in Britain have been banned from administering corporal punishment since 1998. But Ferris Lindsay, the head of six pupil Tyndale, has evaded the ban because he deliberately set up in 1999 to fall outside the legal definition of a school.
The Government has been trying to make Tyndale follow the same rules as independent schools since 2003. But so far, despite two official consultations and 399 letters and emails in 200607 alone, it has made little progress.
Now in the Education and Skills Bill progressing through Parliament, ministers are introducing a new category of "independent educational institution" which would encompass existing independent schools and institutions that only provide part-time education for pupils of compulsory school age but are in other respects independent schools.
To date Tyndale has provided 18 hours tuition a week or less - fewer that the 21 hours a week that government guidance says adds up to full-time education and the definition of an independent school.
But it would fit the new definition of an independent educational institution, and under the new law would have to meet existing standards for independent schools which bar corporal punishment.
The Government's own documents show that Tyndale is one of four institutions which would be affected by the change. Mr Lindsay said: "This to our mind is using a sledgehammer to crack a nut."
The legislation allows the Government to exempt specific types of institutions from the "independent educational institution" category. Government documents accompanying the bill suggest exemptions will include summer schools, hospital schools, LEA home tutorial services and home education.
There is no mention of religious supplementary schools or sports clubs, which could also be affected.
At Tyndale children aged between five to seven can receive a single smack and those between eight and 13 a maximum of three.
Mr Lindsay said the smacks - "hard enough to register but not enough to damage" - were more effective than other long, drawn out punishments.
A qualified teacher with 24 years experience, he said the sanction was employed no more than ten times during the 200607 school year and was only ever given with explicit parental permisssion.
Corporal punishment was a small part of disciplinary policy that also included measures such as being awarded stars for good behaviour.
Ofsted told the education department about smacking at Tyndale as long ago as 2004. Mr Lindsay said no official has raised the matter with him since.