She said information provided by governors and a parents pressure group on the GM bid by Manningtree School had been misleading.
But Mrs Shephard said there were "insufficient grounds" to declare the ballot, which resulted in a "yes" vote, void.
The Department for Education and Employment said some information provided for governors such as the availability of additional funding could have been misunderstood.
It added: "Governors are at liberty to decide the timing and organisation of parental meetings on GM ballots. However, the Secretary of State considers that parents would perhaps have been better informed had these meetings been held earlier in the ballot process."
Mrs Shephard also found that parts of the information provided by a group called Association Against an Independent Manningtree School were misleading and may have reduced the "yes" vote.
Ted Crunden, vice-chair of education with Essex County Council, said he was not surprised by Mrs Shephard's decision.
He said: "We didn't think we were on a level playing field."
But the authority believed its complaints had been vindicated.
Michael Nesbitt, head of Manningtree, said: "We are very pleased with this outcome and this decision reflects our confidence that this is the best way forward."
Lynda Guglielmi, chairman of governors, added: "I am glad that parents, teachers and governors will now be available to continue to work together for the good of the school."