The Government is to investigate whether lotteries to decide admissions to secondary schools harm the children who both win and lose, ministers announced yesterday at the start of the week where September's 11-year-olds and their parents learn their fate.

Letters to the parents of Year 6 children will be sent out this week advising them whether they have secured their first or second choice of secondary school.

But with fewer children than ever getting their preferred choice of school – with one notable exception in the West – education minister Ed Balls has questioned his own Government's controversial initiative to decide with random lotteries.

Mr Balls said his education ministry would look at how lotteries were being used, and questioned the need for schools to do so every year.

But in Wiltshire – the only education authority in the West which had managed to cut the numbers of children not getting their first choice school place – the lottery system is only just being introduced.

At Sheldon School in Chippenham, parents of next year's new intake – the current Year 5 – are bracing themselves for a lottery the school plans to introduce in 2010, one of few schools to do so in the region.

Mr Balls said the lottery system could put twins in different schools, which he said was 'ridiculous'. "Allocating within bands on a lottery or allocating all places on a lottery, I think that most parents would see that as being pretty arbitrary, pretty unfair and very destabilising for their children," he said.

"If there's no other fair differentiator, then a lottery is the only way to do it. But that is absolutely the last resort and you'd expect it to happen on rare occasions, not every year, not for every school and only in a handful of cases," he added.

But if successful, Sheldon's governors plan to use the lottery method every year as the only way of fairly allocating school places. The school shows no signs of becoming less popular and the population of Chippenham is still growing.

Sheldon is the most popular of the town's three secondary schools.

Previous methods used to select pupils came down to distance from home to school – and that meant children from one side of town were not getting a look in.

That will be the case when Chippenham parents, like the half-a-million others nationwide, find out their child's future school, and the stress is overwhelming, according to parents' groups.

Margaret Morrissey, of campaign group Parents Outloud, said it was inevitable that many families will end up disappointed this year. She said: "Parents go through hell this time every year. When they open the letter, if it is good news, they often burst into tears and realise what terrific stress they were under. If it's not good news it will be devastating. There is nothing you can say to parents, it's just devastating.

"I just hope the ministers are proud of themselves for sitting there for another whole year and just ignoring the problem."

Last year the Government brought in a new statutory admissions code to make the process fairer, and the code has just been tightened again.

Ministers said it would help to stamp out unfair practices such as schools interviewing parents and pupils or asking for personal information about their family background in order to select pupils.

But critics suggest it has meant that fewer parents get their first choice, while parents themselves still find the system confusing.

Government-commissioned research, published last month found that parents find the process "complicated, time consuming and stressful."

They want a simplified system, with a standard application form across the country and a single closing date.