Malcolm Beresford, head of Willoughton primary, near Gainsborough in Lincolnshire, was suspended in November. He is a member of the Government's innovation unit and one of 22 heads groomed by the National College for School Leadership for a wider role.
Under Mr Beresford's leadership the 66-pupil primary had more computers than children and a flat management structure which blurred the distinction between teachers and teaching assistants.
When The TES visited the school last summer, Mr Beresford was keen to emphasise that all staff were expected to pitch in with different tasks.
The business and IT manager doubled as teaching assistants, and the caretaker helped out with special needs pupils. Mr Beresford said that he was not above "shovelling cats' mess" in the school grounds.
But some parents had expressed unhappiness with the school and Mr Beresford's leadership in particular.
A Lincolnshire county council spokesman said: "The governing body of Willoughton primary has confirmed that in association with the local education authority they are investigating concerns relating to the leadership and management of the school.
"The headteacher, Malcolm Beresford has been suspended from duty, but (I) need to emphasise that this is a neutral act and has been done so to allow for a full investigation to take place."
The spokesman said the education of children and the life of the school would carry on as usual.
Hazel Belcher, has been seconded from New Leake primary, Boston, to manage the school while the investigation is being carried out.
A spokesman for Mr Beresford's union, the National Association of Head Teachers, said he had no comment to make at this time.
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