The "power to innovate", in which schools can apply to ministers for permission to disapply any law which gets in the way of raising standards, was a key element of last year's Education Act.
But the Department for Education and Skills told The TES this week it had received only two formal applications since last September.
Both were from schools wanting to change the length of their day. This is already allowed in existing legislation, but only if the changes runs from the start of an academic year.
The power to innovate had allowed these two schools to change the length of the day mid-year, said a spokeswoman.
Phil Willis, Liberal Democrat education spokesman, said: "This is a classic example of rhetoric coming down from Number 10 which turns out to be utterly meaningless for the vast majority of schools. Schools want freedom from central control, not further centrally-controlled innovation."
The figures will be a disappointment for the Government's innovations unit, set up last summer . It was designed to promote school-based change and employed a lead director and former head Mike Gibbons, who earns pound;95,000 a year and five directors earning between pound;50,000 and pound;70,000.
The power to innovate is listed first on its website in a catalogue of approaches which schools and education authorities can use to introduce change.
Tollbar business and enterprise college, in north-east Lincolnshire, was told that it could not use the power to change teachers' contracts to give them time off in lieu in return for working up to 4.30pm.
Tollbar runs A-level classes beyond the normal end of school day at 3.15pm as part of its partnership with a local private school and further education college.
But the department advised the school not to apply, because any changes to teachers' contracts would require an agreement with staff or an exemption from employment law. The innovation power only relates to education law.
The school had not consulted staff formally before applying.
David Hampson, principal, said: "This was a waste of time. The new power does not really exist in the way that we wanted to use it."
A DfES spokeswoman said the department was working with 75 schools and eight authorities on a projects. Schools already had a "range of freedoms" to do things differently, and the Government wanted to promote them to ensure that all schools were aware of them.