She told more than 100 delegates at the Association of Grant Maintained and Aided Schools' conference that the 1988 Education Act needed to be "sharpened up" to combat the "slickness" of the anti-GM movement.
"Our role is to make sure as far as we can that there is a fairness of information. I want to make sure that we deliver that," said Mrs Shephard.
A primary headteacher said that schools needed to be supported during the parental ballot on opting out of education authority control. Mrs Shephard acknowledged that heads were often amazed to discover that public meetings on GM status were dominated by anti-GM campaigners.
"People do not have the experience to deal with this. You cannot expect an isolated primary head to cope with this sort of thing," she said, adding that Sir Robert Balchin, chairman of the Grant Maintained Schools Foundation, could offer direct help in difficult situations.
Martin Rogers, spokesman for Local Schools Information, the pressure group which has led the campaign against opting out, rejected Mrs Shephard's claims. "How have they got the audacity to suggest that? If there is any unfairness it is the wrong way round. They have such an overwhelming advantage and the conduct of meetings and campaigns is very largely in the hands of headteachers and governing bodies. We receive constant calls about how they will not have speakers on platforms," Mr Rogers said.
Mr Rogers said many schools held public meetings on opting out only for parents who had pupils at the school and did not allow those who planned to send their children there in a few years' time to attend.
The options for introducing new rules for GM schools are thought to be limited as ministers have ruled out any new legislation in the immediate future.
A spokesman for the Department for Education said there were no plans to issue new rules or guidelines on opting out. Mrs Shephard was simply anxious to ensure that information about opting out was fair on both sides, he said.
The Education Secretary also commented on the sensitive issue of selective GM schools.
She said many schools had become centres of excellence without turning selective. "I would not want to see a GM application as a pretext for wanting selection . . . We do not want a return to selection via GM schools but we will look at every school's application individually . . . There is no blanket policy one way or the other."
Guest speaker Peter Downes, president of the Secondary Heads Association, focused on a SHA paper called "A Better Cake" which highlights the inequalities of funding between schools.
Mr Downes, head of Hinchingbrooke School in Cambridgeshire, gave a detailed example of how two almost identical schools in different counties could have a difference in funding of Pounds 300,000.
"For a Government interested in equity, this is simply not acceptable, " he said.
He also lambasted the School Teachers' Pay Review Body's proposals to pay headteachers an "insulting" Pounds 1,500 one-off bonus payment if they were successful in meeting a series of performance indicators.