Catholic state schools in north Oxfordshire decided to defy the county council over the dates of the Easter holiday.
The schools were due to open this week, along with other state schools in the county.
But Catholic headteachers said it would demean the meaning of Easter by separating the religious break from the two-week school holidays starting April 1.
Oxfordshire and a number of neighbouring councils switched to a six-term school year last September, which meant that after the four-day Easter weekend, children have returned to school for four days before breaking up.
But some Catholic schools claim the system undermines the religious significance of Easter.
David Dawson, head of Blessed George Napier School, in Banbury, said: "We as a Catholic group of schools in the north felt uncomfortable, because we felt it was separating the celebration of the Easter feast from the actual holiday and we could see this as the thin end of the wedge.
"Good Friday was just referred to as another Bank Holiday and we didn't want that to happen. We have a right as church schools to determine our own holidays.
"We've never done this before and we don't like to go against everybody else, but we just felt on a matter of principle this was the right thing to do.
"We planned this a long time ago and parents have been consulted."
St Mary's Primary School in Bicester, St John's Primary and St Joseph's Primary, both in Banbury, were also on holiday, although Catholic primaries in Oxford remained open.
Pupils at St Gregory the Great Catholic School, in Cricket Road and Iffley Turn in Oxford, where Mr Dawson is acting headteacher, were in classes this week, because some staff teach in a consortium of sixth-form teachers, which also serves non-denominational schools.
Tony Crabbe, the county council's executive member for schools, said: "I think it's nonsense to suggest that separating the Easter Bank Holidays and the two-week break devalues the significance of Easter.
"I take the opposite view and do not agree with the course of action these schools have taken.
"It's very disruptive, but these schools do have the right to fix their own holidays and go against our advice."
He said the Catholic schools which were closed this week would return to classes a week earlier than other schools.
A spokesman for Oxfordshire County Council said the authority had advised the Catholic schools not to adopt different dates, because it was concerned that families would find it difficult to plan holidays if they had children at more than one school.
Next year, Easter falls at the end of schools' two-week April holiday, which will run from April 3 to April 17. Easter Sunday will be celebrated on April 16. In 2007 it will be in the middle of the two-week break.
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