The loophole came to light as it was revealed that by 2009 all other aspiring heads will have to have the NPQH before they can even apply for a top school job.
At the moment governors can appoint a head without the qualification. Since April 2004 applicants either had to hold the NPQH or prove they were working towards it, although they are given four years to complete it.
A study carried out in the last academic year found that almost half of primary heads in England and Wales had been appointed before completing the NPQH.
The National College for School Leadership, which administers the course, said rules requiring all new candidates to hold the qualification by 2009 would improve the quality of heads. But it admitted that leaders of the 200 academies that the Government intends to open within the next five years would not be bound by the requirement.
The revelation will fuel mounting criticism of academies - independent state schools, part-funded by business sponsors. It follows complaints last month that academy teachers do not have to register with the General Teaching Council for England.
Steve Sinnott, general secretary of the National Union of Teachers, said:
"It seems extraordinary that academies are championed as the answer to under-achievement in inner cities, yet the people employed there do not even have to adhere to all the same professional standards as those working at other schools."
A spokesman for the Department for Education and Skills said: "Although it is not mandatory for academy heads to hold the NPQH, we would always encourage them to seek the highest standards of professional development."
Recruitment analysts fear new rules surrounding the NPQH will add to growing problems facing schools searching for a headteacher. The TES revealed last month that almost 2,700 schools had to look for a new head last year and a third of posts had to be re-advertised.
But a spokesman for NCSL said: "There is an average intake of 4,700 aspiring headteachers each year to NPQH. This exceeds the 2,700 schools who advertised for a new headteacher in 2004. It provides a substantial reservoir of people who are eligible to apply for headship posts."