The decision to segregate pupils at Scotland's first shared campus had nothing to do with religion, according to the local authority.
Three schools share the new campus
St David's High, a Catholic school, and non-denominational Dalkeith High School were moved onto a single site last week.
Some parents have voiced concerns that pupils are being kept apart at break times.
But Midlothian Council said the religious division between the schools was irrelevant.
Education director Donald MacKay said the decision had been taken to ensure the transition went as smoothly as possible.
And he predicted that the 2,200 pupils would be able to mix freely with each other within the next few weeks.
Dalkeith's new shared campus was widely regarded as a bold attempt to bring down barriers in Scotland's education system.
The site has brought together the town's two secondary schools, along with Saltersgate Special School.
During lunch breaks the pupils at Dalkeith High cannot mix with the Roman Catholic pupils from St David's.
One mother whose son and daughter attend different secondary schools told BBC Scotland that her children had complained about not being allowed to speak to each other in the playground.
She has advised her children to ignore any segregation.
Pupils from different schools have been prevented from mixing at meal times
Mr MacKay said the arrangement was a
"It would be very wrong of us just to let everybody come into the campus and not to have some concern about the safety and well-being of all of the youngsters coming in," he said.
"For some of the youngsters it will be quite a frightening experience, suddenly going from their own secluded school into a very large campus organisation.
"If you suddenly throw youngsters into that without structure and support it could be quite an explosive situation and we want to avoid that."
He said the two schools' management teams were looking at how to make the dining room a more shared area.
"All that I've asked people to do is be a little patient with us in allowing us to get to the next step where people can sit, dine and chat to who they want," he said.
Mr MacKay denied claims that security guards were patrolling the playground to keep pupils apart.
And he said that the different religious backgrounds of the schools had not been a consideration.
He said: "As far as we're concerned, the fact that one is a denominational school and the other is non-denominational is irrelevant.
"It wouldn't have mattered if they were two denominational schools or two schools that were non-denominational - that is not a core issue for us.
"The two schools have a very good track record of working together and have been doing so for years.
"Youngsters have also met for years in the town centre and this has not been a problem."
First Minister Jack McConnell said that the pupils' needs should come first in every school in Scotland.
"There should be no artificial dividing lines or barriers. There should be no unnecessary inflexibilities," he said.
"Everybody should have the opportunity to develop their talents and their potential to the full and if any barrier is ever in the way of that then it should be removed and the pupils should come first."