Edward Osmotherly, the Local Government Ombudsman, criticised as ambiguous some of the admissions criteria.
He said parents were not given good enough guidance on how the criteria operated and did not understand why their children were not offered places at the school of their choice. They were hampered in preparing their applications as the council did not even publish the supplementary criteria used by staff to decide who should go where.
Mr Osmotherly found maladministration causing injustice and recommended that the authority apologise to the five parents who complained to him and pay each Pounds 250.
His recommendation comes less than three years after a previous ombudsman's investigation found that some Hertfordshire admissions criteria were ambiguous and inadequate. That inquiry said there had been failures in the arrangements for informal appeals.
And Mr Osmotherly said: "Parents have an entitlement to know the criteria the authority will use in making decisions about the allocation of places." But although he recognised the bewilderment, suspicion and sense of injustice felt by the parents who complained, Mr Osmotherly did not recommend that the county now provide places at the schools of their choice. He said the authority had gone to great lengths to improve the internal consistency and fairness of the allocation process.
His concerns, however, centred on the allocation of places on the grounds of specific educational or other significant reasons.
Of the five complaints he received, four concerned requests for places at a single-sex girls' schools while the other was a request for a place at a mixed school in a different area of the county.
One parent had even moved house to get nearer to the school she wanted her daughter to attend only to be told she failed to get a place and did not meet the distance criteria.
Mr Osmotherly said it was impossible to know how the parents would have put their case had they been aware of the additional criteria council officials used for allocating places.
And he said: "The complainants will be left with a feeling of injustice since they will never know whether their children would have got the places they wanted but for the maladministration I have identified."
In another investigation, Ombudsman Patricia Thomas rejected a complaint against Tameside borough council from a parent who wanted to get his daughter into a single-sex school.