Education officials were forced into an embarrassing retreat this week after ordering Roman Catholic and Protestant pupils not to mix with each other.
Youngsters at St David's RC high and Dalkeith high, in Midlothian, were warned they would be punished if they talked to each other or sat together in the canteen.
The rule was introduced after the two sets of pupils moved into a shared pound;33 million campus last week. Ironically, the aim of the campus is to stamp out religious bigotry.
Jack McConnell, Scotland's First Minister, claimed last year that bringing schools of different faiths together would "help bring about the long-term change we need to rid us of sectarianism".
But education officials in Midlothian introduced segregation in an attempt to ensure a "smooth introduction" to the new 2,200-pupil campus, amid fears the two groups would fight.
They were forced to back down days later after parents, pupils and anti-sectarian groups condemned the move.
In one family, brother and sister Lee and Lana Brady, aged 16 and 14 respectively and who attend separate schools, were forbidden from speaking to each other.
The 900 pupils at Dalkeith high and 770 at St David's are taught in separate classroom blocks and each school has its own entrance. But they share sports, drama, music and canteen facilities.
The site is also shared with Saltersgate special school.
Lana, who attends St David's, described how a security guard with a walkie-talkie stood by to make sure the pupils did not mix and informed on them if they did.
She said: "No one has been punished yet but we have been threatened with detention.
"I have quite a few friends at Dalkeith high and when the two schools merged I thought it would be great but it's even more difficult to see them now."
Kevin Tierney's 16-year-old daughter Michelle came home from St David's to tell him about the ban.
He said: "She said they had all been told to be nice to the other children and a teacher said they had to love thy neighbour. But that's impossible if they can't even talk to each other."
The anti-sectarian campaign group Nil by Mouth said: "Mixed campus schools are surely all about encouraging children of different faiths to come together and appreciate each other."
Donald Mackay, Midlothian's education director, backed down under pressure.
He said: "We may have been at fault in the early stages.
"We thought we had explained reasonably well why the schools would be separated in the first few days.
"But, with hindsight, I appreciate we could have done it better."
Lord James Douglas-Hamilton, Tory education spokesman, accused the council of "social engineering gone mad".