Nicky Morgan has said she wants to stop the "vexatious" objections so senior staff at faith schools can get on with educating children.
Her plans will mean that only local parents and councils will be able complain that a child has been unfairly overlooked for admission - not organisations such as the Fair Admissions Campaign.
Currently, Christian and other faith schools are - to an extent - allowed to prefer pupils on the basis of their religious background.
This has led to criticism from some Christians and other groups, who argue that it is inherently unfair to prefer a child because of their faith history, and that the process disproportionately ignores poor and ethnic minority children who they argue are most in need of a good education.
The proposals also include reducing the current amount of years before a school's admissions criteria is publicly consulted on, down from every seven years to every four years.
This means if parents in an area have an issue with a school's selection policy, they can voice their views in a public consultation quicker than previously.
Education Secretary Nicky Morgan said: "As part of our mission to deliver educational excellence everywhere we want every child to have the opportunity to go to a good local school by making it easier for parents to have a say in their local school's admission process.
"So that parents can be confident that the school admission process is working for them - we are ensuring only local parents and councils can object to admission arrangements, which will also put a stop to vexatious complaints against faith schools by secularist campaign groups.
"At the same time we will be giving parents a greater voice by requiring admission authorities to consult every 4 years."
