Jacqueline Forsyth, a single parent from Prestwick, had her application rejected by South Ayrshire Council. She now faces possible imprisonment and having her children taken into care, or a fine, if she doesn't send them back to school.
Mrs Forsyth claims the council has breached the Scottish Executive's statutory guidelines by not considering the provision she has in place to educate her children at home. Robin Harper, co-convener of the Green Party, believes this is only the latest example of education authorities dragging their feet over implementing the Executive's 2004 statutory guidelines.
Mr Harper, who recently tabled a parliamentary motion on the matter at the Scottish Parliament, said: "Some councils are not sticking to the letter of the law and should be reviewing their procedures concerning the Executive's guidance over home education."
Mrs Forsyth removed her children from Prestwick Academy and Heathfield primary last April because she felt her sons were being bullied. She wrote to the director of education informing him of her decision, but now realises that she should have waited for permission before taking them out of school.
While waiting for consent, the children suffered from stress and were issued with medical certificates confirming they were unfit to attend school. In October, she was summoned before the attendance council, which was apparently unaware that she had written repeatedly to the council about her decision to home educate.
Her application was rejected in December, and she was notified she would be prosecuted for non-attendance of her two sons.
Chris Ballance, the Green Party MSP who attended a meeting in November between Mrs Forsyth and the education department as an "honest broker", was surprised by what he describes as the council's inflexibility Figures from South Ayrshire show that the council has received 18 applications from parents to educate their children at home, and only one was refused.
"That in itself suggests that they were making an exception of Mrs Forsyth for some reason," Mr Ballance said.
Mrs Forsyth has no regrets. "The boys are so happy, their confidence is coming back. It's been hard, worrying if I am getting their education to where they should be, but they were behind when they left school. They are getting there, and they are beginning to enjoy being educated."
Mr Harper pointed out: "It is not the duty of the school to educate children but the duty of the parents to ensure their child is being educated. So when parents take their children out of school to educate them, all they are doing is complying with their duty in law."
A spokeswoman for Schoolhouse said: "Although the statutory guidance for local authorities has been in place for almost two years, we remain extremely concerned about the postcode lottery which still exists.
"Families should not have to put up with misleading and inaccurate information from any public body, yet we have clear evidence that this is still the case in some council areas where there is open hostility to home education."
A spokesperson for South Ayrshire said: "Each application for permission to home school a child made by a parent or guardian is looked at on an individual basis. The most important aspect of this process is to ensure that any decisions that are taken are in the best interests of the child.
"It is not possible to comment on specific applications as this would breach confidentiality."
Official statistics show that 544 children were educated at home last year.
But this is the figure known to local authorities and Schoolhouse claims the true total could be over 5,000.