According to Le Figaro the supermarket giant took this move in response to customer concerns.
Leclerc regards the measure as " pioneering ".
The move follows the announcement of a government scheme last month to combat child obesity, and is said to be a direct response to the campaign and its goal to reduce the number of fattening snacks and foods marketed at children next to checkout counters.
A government website confirms that 14.3 per cent of children in France are considered overweight and 3.5 per cent obese.
These represent some of the lowest rates in Europe (along with Sweden and the Netherlands), but nonetheless considered too high given the health problems associated such as diabetes.
In February Health Minister Roselyne Bachelot presented three new measures to help reduce childhood obesity.
One of these includes the withdrawal of confectionery and sugary products from supermarket checkout counters by the end of June this year.
A meeting of stakeholders was called for to agree a way forward.
Leclerc is aiming to have withdrawn its selected brands by June 1.
They will be moved back to the main confectionary aisle.
The sweets mainly concerned will include Ferrero, Kinder and Haribo brands.
Le Figaro confirms that they will probably be replaced by treats without sugar, mostly for adults.
TFI quotes Michel-Edouard Leclerc, the supermarket chain's President, as saying that the supermarket sells 18.5 per cent of confectionery sold in supermarkets in France.
With products near the checkouts comprising 20 per cent of these sales, Leclerc predicts that the supermarket chain will loose about €5m a year by this change, the news channel said.
However, a Leclerc spokesperson did not respond to ConfectioneryNews.com in time for publication.
Ferrero, Kinder and Haribo all refused to comment.
Leclerc has angered some industry players by acting unilaterally.
The president of the Association nationale des industries alimentaires (national association of food industries) is calling for a common position agreed by manufacturers, retailers and the government.
Le Figaro quotes Jérôme Bédier, president of the Fédération des entreprises du commerce et de la distribution (federation of commercial businesses and retailers) as saying that he wasn't sure children would eat less sweets and chocolate if they are removed from beside the checkouts.
Another element of the national anti-obesity plan is the suppression of publicity for certain sugary foods and drinks during young people's media programmes.
A survey conducted by the Health ministry showed that that nearly half of children would like to consume publicised products and 91 per cent of children said they managed to get their parents to buy them.
If stakeholders cannot agree and abide by a solution the government is prepared to legislate to achieve this goal.
The plan also demands that by September 2008 the quality of school meals is improved without excessive cost and meals are planned well in advance.