Although the number of complaints fell from 245 in 2005/06 to 173 in 2006/07, the figure rose sharply to 369 in 2007/08.
Despite this, the report found local authorities and church diocesan panels complied with the Schools Admissions Appeals Code "in almost all respects".
The Reverend Janina Ainsworth, chief education officer for the Church of England, welcomed the report and said it gave local authorities and governing bodies a chance to revisit their admissions policies.
She said: "We are grateful for the work that has taken place at a local level to correct any previous technical errors and to clarify any unclear aspects within admissions policies."
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