WIRRAL was forced to rethink its school admissions policy after the High Court upheld a ruling that its method of allocating pupils to its 23 secondaries was "unfair".
The decision affected the choices of the 4,000 children due to start at secondary school this September, and the council was disappointed at losing the case.
Admissions arrangements for entry to secondary schools in the borough for this September had been unanimously agreed by the education committee.
The council had claimed the policy had been formulated after a lengthy consultation exercise. It argued that it was the fairest available system of allocating places. But the adjudicator disagreed.
Under Wirral's disputed policy, parents who selected a grammar as their first choice had their second choice of school "elevated" (ie treated as if they had put i as a first choice) if their child failed the 11-plus.
The head of St Mary's College, Wallasey, objected to the policy saying it gave some parents an unfair advantage, because they effectively had two "first choices".
The complaint was upheld by the adjudicator in November and in December the High Court rejected the council's claims that the adjudicator's decision was irrational.
Further allegations that the adjudicator had exceeded his powers and had breached natural justice by failing to consult the council properly were also dismissed.
Mick Groves, education chair, was disappointed that the council's lawyers had failed to convince the judge and said: "Reluctantly now we must accept the outcome."
Under new amended arrangements, when the council considers parental preferences for secondary school, they are considered in the order stated.
It is not now possible to "elevate" a second preference for a comprehensive school.