France has launched a nationwide investigation into babies born with missing upper limbs after the discovery of nearly a dozen new suspected cases.

The national health agency had initially dismissed claims that a cluster of seven infants born with abnormalities in the Ain area near the Swiss border was abnormally high.

However, after 11 further cases of babies born with missing or deformed arms and hands were identified, the agency’s head, François Bourdillon, said a full investigation was under way.

“We will look at all the suspect cases,” Bourdillon said, adding that the results would be known in three months.

France’s health minister, Agnès Buzyn, last week said she and the environment minister, François de Rugy, would look more closely at possible causes for babies being born without hands or arms since 2007. She said it was unacceptable that no cause had been found.

An investigation by Santé Publique France, the national health agency, published at the beginning of October, suggested the number of babies born with these abnormalities in the Loire-Atlantique and Brittany regions constituted worrying clusters.

But it insisted the number of cases in Ain was not above average and declared any further investigation closed, suggesting the incidences were probably down to chance.

Scientists and researchers disputed this conclusion, claiming there had been 58 times the expected level of these abnormalities in Ain.

Full research into the scale of the problem and possible causes has been hampered by the lack of a national register of infant deformities.

News of the national investigation has vindicated the work of Remera, the publicly funded organisation that has documented and researched cases in the Rhône-Alpes region, including Ain. It had ruled out genetic malformations as well as drug- or alcohol-related causes after speaking to the affected parents and their doctors.

Emmanuelle Amar, the director of Remera, said the chance of the abnormalities being coincidental was “more than infinitesimal” and criticised the lack of action by the authorities as a “health scandal”.

Researchers say the only common factor in the cases was that the infants’ parents lived in rural areas, throwing suspicion on pesticides and environmental factors.

“These malformations are very rare, but also very specific. There is something, some product, that is cutting the limbs at the time the embryo is developing. We must search for it,” Amar told the Guardian.

Amar – who raised the alarm over the abnormality cluster – and her team have since had their funding removed and received redundancy letters.

Santé Publique France claims an average 150 babies are born each year in France with such birth anomalies, but critics say the figure is based on incomplete data and covers only 19% of France.