Julie Wales, from Dalry in North Ayrshire, said SNP legislation limiting P1 classes to 25 meant her three daughters could not go to the same school.
The situation has arisen because Mrs Wales works in Glasgow, where she lectures at Langside College, and chose to send her eldest daughter Xanthe to nearby Battlefield Primary School, on the south side of the city, two years ago.
However, when she applied for her second child Orlaith to attend the same school her placing request was rejected because classes are now capped at 25 and priority is given to children in the catchment area.
It is unlikely her youngest daughter Laureli, who is currently at nursery, will be able to get into Battlefield when she reaches school age.
That has left the 42-year-old senior lecturer with the prospect of either splitting her children up or moving her eldest daughter out of Battlefield, where she has been happy for the past two years.
"I made what I thought was a safe choice by sending my eldest daughter to Battlefield because it was close to my work and allowed me to drop her off and go to work on time," she said.
"Now it is time to send my five-year-old to school I have been told there is no space for her because of the current rules.
"It is hugely worrying because it means I either have to pay for a private child minder to look after her until her local school opens while commuting with the others, or remove my eldest child from school and force her to start again somewhere else."
Mrs Wales said she could understand if legislation had reduced class sizes to 18, as the Government had originally intended, because such a reduction would make a significant difference to the quality of education on offer.
"It is obvious that I am a fly in the ointment of the Government aims, but capping classes at 25 serves no obvious purpose and it is actually restricting parental choice," she said.
"I am a long-term taxpayer who believes that my children should be treated with a little more care than to be prised apart and have the rug pulled out in these vital early years."
However, a Scottish Government spokeswoman defended its class size policy. "Parental choice, and in particular the right to make a placing request, is something the Scottish Government supports and it is up to individual local authorities to determine these," she said.
"The first year of school is vitally important, which is why a limit of 25 pupils was set for P1 classes in 2010 and has allowed teachers to expect consistency and develop their teaching style accordingly."