Local authorities, however, are being asked to treat requests sensitively until fresh legislation is brought in. Sheriff courts will remain the final arbiter if disputes arise.
The issue was first raised by Glasgow last autumn after it suspected a conflict between the 1980 Education Act and the Standards in Scotland's Schools etc Act, passed last summer. Lawyers have now confirmed the new Act failed to tidy up the previous legislation.
"The only way of wholly remedying this anomaly is through primary legislation and we will take the first opportunity to do this," Jeane Freeman, head of the Executive's school standards and improvement division, says in advice to directors of education.
The issue is now a pressing matter as authorities begin to take entries for primary 1 classes next session.
Ms Freeman says that ministers wanted to make it clear that parents cannot submit a placing request for a child of under 4 years 6 months, although many go to school at that age. But the latest Act, in amending the 1980 legislation, says only that children should be "of school age", defined in th earlier Act as being between five and 16.
"We agree with this interpretation that it is not now valid for a parent of a child aged between four and a half and five to make a request under the placing request legislation for entry to primary school," Ms Freeman says.
In a qualifying statement, she believes it is reasonable to infer that a child should be five at the date of entry to the school and not at the date the request is made.
A third change rules out a request to another school while an under-five is in P1. Parents can, however, make a request for entry to P2 even if their child entered first year before the age of five.
Ms Freeman makes it clear parents of under-fives should be able to say which school they want their child to attend, even if they are outwith the current legislation and will be unable to appeal against an authority's refusal.
Ian McDonald, depute director of education in Glasgow, said: "The letter recognises there is a serious problem and I accept there is no immediate solution. It will leave local authorities with a major headache in how to deal with placing requests and hundreds of families could be disadvantaged. I hope the Scottish Executive will have the opportunity to rectify this oversight or error."
The city receives some 1,800 placing requests for entry to P1, half from parents of children under five.