Three families have launched legal action after being told they could not get their children into the popular Roseburn Primary.
Their children, who live just outside the catchment area, all attend the nursery at Roseburn, but face being separated from their friends because the school will only have one primary one class this year instead of the expected two.
After losing at the appeals committee stage last week, the three families opted to take their case to the Sheriff Court in a bid to force the council to run two classes. Now they have accused council bosses of trying to put them off taking legal action after receiving a "threat" from the authority's legal department warning that they might end up having to pay all the costs if the council's position is upheld.
The council's principal solicitor e-mailed one of the parents to say: "I understand that generally in education appeal cases the council does not insist on seeking expenses in the event of their position being upheld by the court.
"However, the council consider each appeal on a case by case basis depending on the nature and conduct of each litigation and no absolute policy applies."
The e-mail went on to advise parents that they should not represent themselves and should seek proper legal advice or face "significant legal problems".
This week, the council's solicitor refused to accept the writ from Roseburn parent Pete Gregson, who is set to represent the three families in court, because he is not one of the three parties taking the action.
The parents feel they are being intimidated by the council, and claim that its legal team is trying to put them off going to court.
Landscaper David Simpson, 34, who lives just half a street out of the Roseburn catchment area and is trying to get his daughter Carolina, four, into the school, said: "They are saying that if we do go ahead with legal action, it will cost us substantial legal fees. They are trying to put us off. It's our right to challenge them, regardless of cost."
His wife Patricia, who received an e-mail from the council solicitor, said: "They sent me an e-mail saying that if I took it to the Sheriff Court, it could have significant legal consequences for me and I feel that that is a threat."
Mr Gregson, who has a son going into primary one at Roseburn, added: "It's a disgrace. It's not only the cost of the case but their demands that they pay extra money to go through a solicitor They are trying to frighten these parents."
A council spokeswoman said: "We tried to help the parents by advising them to seek proper legal advice."